When three traits make a line: evolution of phenotypic plasticity and genetic assimilation through linear reaction norms in stochastic environments

Genetic assimilation emerges from selection on phenotypic plasticity. Yet, commonly used quantitative genetics models of linear reaction norms considering intercept and slope as traits do not mimic the full process of genetic assimilation. We argue that intercept–slope reaction norm models are insufficient representations of genetic effects on linear reaction norms and that considering reaction norm intercept as a trait is unfortunate because the definition of this trait relates to a specific environmental value (zero) and confounds genetic effects on reaction norm elevation with genetic effects on environmental perception. Instead, we suggest a model with three traits representing genetic effects that, respectively, (i) are independent of the environment, (ii) alter the sensitivity of the phenotype to the environment and (iii) determine how the organism perceives the environment. The model predicts that, given sufficient additive genetic variation in environmental perception, the environmental value at which reaction norms tend to cross will respond rapidly to selection after an abrupt environmental change, and eventually becomes equal to the new mean environment. This readjustment of the zone of canalization becomes completed without changes in genetic correlations, genetic drift or imposing any fitness costs of maintaining plasticity. The asymptotic evolutionary outcome of this three‐trait linear reaction norm generally entails a lower degree of phenotypic plasticity than the two‐trait model, and maximum expected fitness does not occur at the mean trait values in the population.     

The chloroplast triggers developmental reprogramming when mutS HOMOLOG1 is suppressed in plants

Multicellular eukaryotes demonstrate nongenetic, heritable phenotypic versatility in their adaptation to environmental changes. This inclusive inheritance is composed of interacting epigenetic, maternal, and environmental factors. Yet-unidentified maternal effects can have a pronounced influence on plant phenotypic adaptation to changing environmental conditions. To explore the control of phenotypy in higher plants, we examined the effect of a single plant nuclear gene on the expression and transmission of phenotypic variability in Arabidopsis (Arabidopsis thaliana). MutS HOMOLOG1 (MSH1) is a plant-specific nuclear gene product that functions in both mitochondria and plastids to maintain genome stability. RNA interference suppression of the gene elicits strikingly similar programmed changes in plant growth pattern in six different plant species, changes subsequently heritable independent of the RNA interference transgene. The altered phenotypes reflect multiple pathways that are known to participate in adaptation, including altered phytohormone effects for dwarfed growth and reduced internode elongation, enhanced branching, reduced stomatal density, altered leaf morphology, delayed flowering, and extended juvenility, with conversion to perennial growth pattern in short days. Some of these effects are partially reversed with the application of gibberellic acid. Genetic hemicomplementation experiments show that this phenotypic plasticity derives from changes in chloroplast state. Our results suggest that suppression of MSH1, which occurs under several forms of abiotic stress, triggers a plastidial response process that involves nongenetic inheritance.     

Gene-environment interactions in atherosclerosis

The importance of environment and genetics working together to shape an individual's risk for atherosclerosis seems intuitively obvious. However, it is only recently that research strategies have begun to evolve that attempt to answer questions related to apportionment of risk that is due to specific environmental and genetic factors. These factors may impact upon risk either singly or, more likely, through a complex interaction that affects the metabolic history of the whole organism. Because the genetic bases of lipid and lipoprotein metabolism have been well-studied, and because of the epidemiologic and pathobiochemical associations between genetic disorders of lipid metabolism and atherosclerosis, researchers have searched for gene-environment interactions within animal and human systems in which the phenotype is defined by some index of lipoprotein metabolism. From work done in the lipoprotein area to this point a clear case can be made for: 1) the genetic influence over the phenotypic response to an environmental stimulus; 2) the environmental modulation of the phenotypic expression of severe genetic defects. In the realm of gene-environment interactions that affect lipoprotein phenotype, diet is the best-studied environmental factor.     

水稻籽粒淀粉分支酶活性的遗传分析

用由247个株系组成的珍汕97B/密阳46重组自交系群体及其含207个分子标记的连锁图谱,在2002年和2003年分别测定亲本和重组自交系群体开花后10 d和20 d籽粒的淀粉分支酶的活性,检测到3个控制开花后10 d Q酶活性的主效应QTL(qnantitative trait loci),联合贡献率为10%,其中qQ10-6与环境发生显著的互作;分别检测到5对和2对染色体区间对开花后10 d、20 d Q酶活性的影响具有加性×加性上位性作用,其中开花后10 d的3对染色体区间具有显著的上位性×环境互作效应.由此可见,水稻籽粒Q酶活性相关基因的表达,受到环境因子的极大影响.     

Environmental stress, inbreeding, and the nature of phenotypic and genetic variance in Drosophila melanogaster

Fifty-two lines of Drosophila melanogaster founded by single-pair population bottlenecks were used to study the effects of inbreeding and environmental stress on phenotypic variance, genetic variance and survivorship. Cold temperature and high density cause reduced survivorship, but these stresses do not cause repeatable changes in the phenotypic variance of most wing morphological traits. Wing area, however, does show increased phenotypic variance under both types of environmental stress. This increase is no greater in inbred than in outbred lines, showing that inbreeding does not increase the developmental effects of stress. Conversely, environmental stress does not increase the extent of inbreeding depression. Genetic variance is not correlated with environmental stress, although the amount of genetic variation varies significantly among environments and lines vary significantly in their response to environmental change. Drastic changes in the environment can cause changes in phenotypic and genetic variance, but not in a way reliably predicted by the notion of 'stress'.     

Multivariate structure of human populations: sedentary versus migrants

The rate change of gene frequency in a population subject to emigration obviously depends on differences in the effective reproductive size (and resulting random genetic drift effects) between emigrants and natives. An important additional force may be the different selection pressures of the original and the new environment into which the population penetrates. Discrete traits and monolocus systems have been studied in many natural populations of various species. However, knowledge about the migration influence on quantitative, i.e. polygenic, characters is very limited. The present study set out to answer the following biological questions: (1) Does migration induce changes in sets of phenotypic, genetic and environmental correlations? (2) If so, are these changes expressed in levels and/or structure of the correlation matrices? Data on 20 anthropometric traits in 305 Mexican families [129 families from Mexico (sedentary population) and 176 families living in Texas (migrant population)] were used for analysis. The curves of distribution and average values of phenotypic, genetic and environmental correlations remained unchanged between the two populations. However, qualitatively (i.e., as far as the agreement between matrix compositions is concerned), all three matrices changed significantly. The phenotypic correlations appear to be the most highly canalized, the correspondence between the two matrices being 62.1%. The environmental matrices had the highest variation, and although 26.3% of the correlations were in agreement, this was statistically nonsignificant. The most important finding in the present study was the relatively low correspondence between the two genetic matrices (35.6%). We suggest that these changes were provoked by preselection (i.e., by a nonrandom sample) of migrating individuals.     

Effects of genetics and light environment on colour expression in threespine sticklebacks

The genetic basis of traits that are under sexual selection and that are involved in recognizing conspecific mates is poorly known, even in systems in which the phenotypic basis of these traits has been well studied. In the present study, we investigate genetic and environmental influences on nuptial colour, which plays important roles in sexual selection and sexual isolation in species pairs of limnetic and benthic threespine sticklebacks ( Gasterosteus aculeatus species complex). Previous work demonstrated that colour differences among species correlate to differences in the ambient light prevalent in their mating habitat. Red fish are found in clear water and black fish in red-shifted habitats. We used a paternal half-sib split-clutch design to investigate the genetic and environmental basis of nuptial colour. We found genetic differences between a red and a black stickleback population in the expression of both red and black nuptial colour. In addition, the light environment influenced colour expression, and genotype by environment interactions were also present. We found evidence for both phenotypic and genetic correlations between our colour traits; some of these correlations are in opposite directions for our red and black populations. These results suggest that both genetic change and phenotypic plasticity underlie the correlation of male colour with light environment.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 663–673.     

Morphing the hyomandibular skeleton in development and evolution

How might changes in developmental regulatory pathways underlie evolutionary changes in morphology? Here we focus on a particular pathway regulated by a secreted, signaling peptide, Endothelin1 (Edn1). Developmental genetic analyses show the Edn1-pathway to be crucial for hyomandibular patterning, and we discuss our work with zebrafish suggesting how the signal may function in regulating numbers of skeletal elements, their sizes and their shapes. We then review a broader collection of comparative studies that examine morphological evolution of a subset of the same skeletal elements-the opercular-branchiostegal series of bones of the hyoid arch. We find that phenotypic changes in zebrafish mutants copy evolutionary changes that recur along many actinopterygian lineages. Hence the developmental genetic studies are informative for providing candidate pathways for macroevolution of facial morphology, as well as for our understanding of how these pathways work.     

Genetic,phenotypic, and environmental correlations in black medic,Medicago lupulina L., grown in three different environments

We have investigated the relationship between phenotypic and genetic correlations among a large number of quantitative traits (36) in three different environments in order to determine their degree of disparity and whether phenotypic correlations could be substituted for their genetic counterparts whatever the environment. We also studied the influence of the environment on genetic and phenotypic correlations. Twenty accessions (full-sib families) ofMedicago luPulina were grown in three environments. In two of these two levels of environmental stress were generated by harvesting plants at flowering and by growing plants in competition with barley, respectively. A third environment, with no treatment, was used as a control with no stress. Average values of pod and shoot weight indicate that competition induces the highest level of stress. The genetic and phenotypic correlations among the 36 traits were compared. Significant phenotypic correlations were obtained easily, while there was no genetic variation for 1 or the 2 characters being correlated. The large positive correlation between the genetic and phenotypic correlation matrices indicated a good proportionality between genetic and phenotypic correlations matrices but not their similarity. In a given environment, when only those traits with a significant genetic variance were taken into account, there were still differences between genetic and phenotypic correlations, even when levels of significance for phenotypic correlations were lowered. Consequently, it is dangerous to substitute phenotypic correlations for genetic correlations. The number of traits that showed genetic variability increased with increasing environmental stress, consequently the number of significant genetic correlations also increased with increasing environmental stress. In contrast, the number of significant phenotypic correlations was not influnced by the environment. The structures of both phenotypic and genetic matrices, however, depended on the environment, and not in the same way for both matrices.     

Avoiding extinction under nonlinear environmental change: models of evolutionary rescue with plasticity

Rapid environmental changes are putting numerous species at risk of extinction. For migration-limited species, persistence depends on either phenotypic plasticity or evolutionary adaptation (evolutionary rescue). Current theory on evolutionary rescue typically assumes linear environmental change. Yet accelerating environmental change may pose a bigger threat. Here, we present a model of a species encountering an environment with accelerating or decelerating change, to which it can adapt through evolution or phenotypic plasticity (within-generational or transgenerational). We show that unless either form of plasticity is sufficiently strong or adaptive genetic variation is sufficiently plentiful, accelerating or decelerating environmental change increases extinction risk compared to linear environmental change for the same mean rate of environmental change.     

A statistical model for testing the pleiotropic control of phenotypic plasticity for a count trait

The differences of a phenotypic trait produced by a genotype in response to changes in the environment are referred to as phenotypic plasticity. Despite its importance in the maintenance of genetic diversity via genotype-by-environment interactions, little is known about the detailed genetic architecture of this phenomenon, thus limiting our ability to predict the pattern and process of microevolutionary responses to changing environments. In this article, we develop a statistical model for mapping quantitative trait loci (QTL) that control the phenotypic plasticity of a complex trait through differentiated expressions of pleiotropic QTL in different environments. In particular, our model focuses on count traits that represent an important aspect of biological systems, controlled by a network of multiple genes and environmental factors. The model was derived within a multivariate mixture model framework in which QTL genotype-specific mixture components are modeled by a multivariate Poisson distribution for a count trait expressed in multiple clonal replicates. A two-stage hierarchic EM algorithm is implemented to obtain the maximum-likelihood estimates of the Poisson parameters that specify environment-specific genetic effects of a QTL and residual errors. By approximating the number of sylleptic branches on the main stems of poplar hybrids by a Poisson distribution, the new model was applied to map QTL that contribute to the phenotypic plasticity of a count trait. The statistical behavior of the model and its utilization were investigated through simulation studies that mimic the poplar example used. This model will provide insights into how genomes and environments interact to determine the phenotypes of complex count traits.     

INTERACTING PHENOTYPES AND THE EVOLUTIONARY PROCESS: I. DIRECT AND INDIRECT GENETIC EFFECTS OF SOCIAL INTERACTIONS

Interacting phenotypes are traits whose expression is affected by interactions with conspecifics. Commonly-studied interacting phenotypes include aggression, courtship, and communication. More extreme examples of interacting phenotypes—traits that exist exclusively as a product of interactions—include social dominance, intraspecific competitive ability, and mating systems. We adopt a quantitative genetic approach to assess genetic influences on interacting phenotypes. We partition genetic and environmental effects so that traits in conspecifics that influence the expression of interacting phenotypes are a component of the environment. When the trait having the effect is heritable, the environmental influence arising from the interaction has a genetic basis and can be incorporated as an indirect genetic effect. However, because it has a genetic basis, this environmental component can evolve. Therefore, to consider the evolution of interacting phenotypes we simultaneously consider changes in the direct genetic contributions to a trait (as a standard quantitative genetic approach would evaluate) as well as changes in the environmental (indirect genetic) contribution to the phenotype. We then explore the ramifications of this model of inheritance on the evolution of interacting phenotypes. The relative rate of evolution in interacting phenotypes can be quite different from that predicted by a standard quantitative genetic analysis. Phenotypic evolution is greatly enhanced or inhibited depending on the nature of the direct and indirect genetic effects. Further, unlike most models of phenotypic evolution, a lack of variation in direct genetic effects does not preclude evolution if there is genetic variance in the indirect genetic contributions. The available empirical evidence regarding the evolution of behavior expressed in interactions, although limited, supports the predictions of our model.     

The ecology of an adaptive radiation of three‐spined stickleback from North Uist,Scotland

There has been a large focus on the genetics of traits involved in adaptation, but knowledge of the environmental variables leading to adaptive changes is surprisingly poor. Combined use of environmental data with morphological and genomic data should allow us to understand the extent to which patterns of phenotypic and genetic diversity within a species can be explained by the structure of the environment. Here, we analyse the variation of populations of three‐spined stickleback from 27 freshwater lakes on North Uist, Scotland, that vary greatly in their environment, to understand how environmental and genetic constraints contribute to phenotypic divergence. We collected 35 individuals per population and 30 abiotic and biotic environmental parameters to characterize variation across lakes and analyse phenotype–environment associations. Additionally, we used RAD sequencing to estimate the genetic relationships among a subset of these populations. We found a large amount of phenotypic variation among populations, most prominently in armour and spine traits. Despite large variation in the abiotic environment, namely in ion composition, depth and dissolved organic Carbon, more phenotypic variation was explained by the biotic variables (presence of predators and density of predator and competitors), than by associated abiotic variables. Genetic structure among populations was partly geographic, with closer populations being more similar. Altogether, our results suggest that differences in body shape among stickleback populations are the result of both canalized genetic and plastic responses to environmental factors, which shape fish morphology in a predictable direction regardless of their genetic starting point.     

The evolution of phenotypic polymorphism: randomized strategies versus evolutionary branching

A population is polymorphic when its members fall into two or more categories, referred to as alternative phenotypes. There are many kinds of phenotypic polymorphisms, with specialization in reproduction, feeding, dispersal, or protection from predators. An individual's phenotype might be randomly assigned during development, genetically determined, or set by environmental cues. These three possibilities correspond to a mixed strategy of development, a genetic polymorphism, and a conditional strategy. Using the perspective of adaptive dynamics, I develop a unifying evolutionary theory of systems of determination of alternative phenotypes, focusing on the relative possibilities for random versus genetic determination. The approach is an extension of the analysis of evolutionary branching in adaptive dynamics. It compares the possibility that there will be evolutionary branching, leading to genetic polymorphism, with the possibility that a mixed strategy evolves. The comparison is based on the strength of selection for the different outcomes. An interpretation of the resulting criterion is that genetic polymorphism is favored over random determination of the phenotype if an individual's heritable genotype is an adaptively advantageous cue for development. I argue that it can be helpful to regard genetic polymorphism as a special case of phenotypic plasticity.     

Reverse evolution of fitness in Drosophila melanogaster

Abstract The evolution of fitness is central to evolutionary theory, yet few experimental systems allow us to track its evolution in genetically and environmentally relevant contexts. Reverse evolution experiments allow the study of the evolutionary return to ancestral phenotypic states, including fitness. This in turn permits well‐defined tests for the dependence of adaptation on evolutionary history and environmental conditions. In the experiments described here, 20 populations of heterogeneous evolutionary histories were returned to their common ancestral environment for 50 generations, and were then compared with both their immediate differentiated ancestors and populations which had remained in the ancestral environment. One measure of fitness returned to ancestral levels to a greater extent than other characters did. The phenotypic effects of reverse evolution were also contingent on previous selective history. Moreover, convergence to the ancestral state was highly sensitive to environmental conditions. The phenotypic plasticity of fecundity, a character directly selected for, evolved during the experimental time frame. Reverse evolution appears to force multiple, diverged populations to converge on a common fitness state through different life‐history and genetic changes.     

Adaptive and nonadaptive plasticity in changing environments: Implications for sexual species with different life history strategies

Populations adapt to novel environmental conditions by genetic changes or phenotypic plasticity. Plastic responses are generally faster and can buffer fitness losses under variable conditions. Plasticity is typically modeled as random noise and linear reaction norms that assume simple one‐to‐one genotype–phenotype maps and no limits to the phenotypic response. Most studies on plasticity have focused on its effect on population viability. However, it is not clear, whether the advantage of plasticity depends solely on environmental fluctuations or also on the genetic and demographic properties (life histories) of populations. Here we present an individual‐based model and study the relative importance of adaptive and nonadaptive plasticity for populations of sexual species with different life histories experiencing directional stochastic climate change. Environmental fluctuations were simulated using differentially autocorrelated climatic stochasticity or noise color, and scenarios of directional climate change. Nonadaptive plasticity was simulated as a random environmental effect on trait development, while adaptive plasticity as a linear, saturating, or sinusoidal reaction norm. The last two imposed limits to the plastic response and emphasized flexible interactions of the genotype with the environment. Interestingly, this assumption led to (a) smaller phenotypic than genotypic variance in the population (many‐to‐one genotype–phenotype map) and the coexistence of polymorphisms, and (b) the maintenance of higher genetic variation—compared to linear reaction norms and genetic determinism—even when the population was exposed to a constant environment for several generations. Limits to plasticity led to genetic accommodation, when costs were negligible, and to the appearance of cryptic variation when limits were exceeded. We found that adaptive plasticity promoted population persistence under red environmental noise and was particularly important for life histories with low fecundity. Populations producing more offspring could cope with environmental fluctuations solely by genetic changes or random plasticity, unless environmental change was too fast.     

Genetic structure of phenotypic robustness in the collaborative cross mouse diallel panel

Developmental stability and canalization describe the ability of developmental systems to minimize phenotypic variation in the face of stochastic micro‐environmental effects, genetic variation and environmental influences. Canalization is the ability to minimize the effects of genetic or environmental effects, whereas developmental stability is the ability to minimize the effects of micro‐environmental effects within individuals. Despite much attention, the mechanisms that underlie these two components of phenotypic robustness remain unknown. We investigated the genetic structure of phenotypic robustness in the collaborative cross (CC) mouse reference population. We analysed the magnitude of fluctuating asymmetry (FA) and among‐individual variation of cranial shape in reciprocal crosses among the eight parental strains, using geometric morphometrics and a diallel analysis based on a Bayesian approach. Significant differences among genotypes were found for both measures, although they were poorly correlated at the level of individuals. An overall positive effect of inbreeding was found for both components of variation. The strain CAST/EiJ exerted a positive additive effect on FA and, to a lesser extent, among‐individual variance. Sex‐ and other strain‐specific effects were not significant. Neither FA nor among‐individual variation was associated with phenotypic extremeness. Our results support the existence of genetic variation for both developmental stability and canalization. This finding is important because robustness is a key feature of developmental systems. Our finding that robustness is not related to phenotypic extremeness is consistent with theoretical work that suggests that its relationship to stabilizing selection is not straightforward.