The contribution of spontaneous mutation to variation in environmental response in Arabidopsis thaliana: responses to nutrients

Fitness effects of spontaneous mutations in a warming world

Spontaneous mutations fuel evolutionary processes and differ in consequence, but the consequences depend on the environment. Biophysical considerations of protein thermostability predict that warm temperatures may systematically increase the deleteriousness of mutation. We sought to test whether mutation reduced fitness more when measured in an environment that reflected climate change projections for temperature. We investigated the effects of spontaneous mutations on life history, size, and fitness in 21 mutation accumulation lines and 12 control lines of Daphnia pulex at standard and elevated (+4℃) temperatures. Warmer temperature accelerated life history and reduced body length and clutch sizes. Mutation led to reduced mean clutch sizes and fitness estimates at both temperatures. We found no evidence of a systematic temperature–mutation interaction on trait means, although some lines showed evidence of beneficial mutation at one temperature and deleterious mutation at the other. However, trait variances are also influenced by mutation, and we observed increased variances due to mutation for most traits. For variance of the intrinsic rate of increase and some reproductive traits, we found significant temperature–mutation interactions, with a larger increase due to mutation in the warmer environment. This suggests that selection on new mutations will be more efficient at elevated temperatures.

Induced mutations alter patterns of quantitative variation, phenotypic integration, and plasticity to elevated CO2 in Arabidopsis thaliana

A key step toward predicting responses to climate change is characterizing genetic variation in populations. While short-term responses will likely be shaped by currently available genetic variation, longer-term evolutionary responses will depend on the supply of novel variation by, ultimately, mutation. Studying mutational contributions to phenotypic variation can provide insights into the extent of potential variation on which selection may operate in future human-altered environments. Here we used the chemical mutagen ethyl methanesulfonate (EMS) to explore mutational contributions to phenotypic variation, integration, and plasticity to elevated carbon dioxide (eCO₂) in three accessions of Arabidopsis thaliana. We found that (1) mutagenesis increased broad-sense heritabilities and variation in plasticity to eCO₂ (genotype by environment interactions); (2) mutational effects varied among the three genetic backgrounds; (3) induced mutations had non-random (biased) effects on patterns of phenotypic integration. To our knowledge, this is the first study to address the effects of chemically induced mutations on phenotypic plasticity to eCO₂ in a model plant. We discuss our results in light of emerging insights from theoretical and empirical quantitative genetics, suggest potential avenues of research, and identify approaches that may help advance our understanding of climate-driven evolution in plants.

Effects of mutation and selection on plasticity of a promoter activity in Saccharomyces cerevisiae

Phenotypic plasticity is an evolvable property of biological systems that can arise from environment-specific regulation of gene expression. To better understand the evolutionary and molecular mechanisms that give rise to plasticity in gene expression, we quantified the effects of 235 single-nucleotide mutations in the Saccharomyces cerevisiae TDH3 promoter (P_TDH3 ) on the activity of this promoter in media containing glucose, galactose, or glycerol as a carbon source. We found that the distributions of mutational effects differed among environments because many mutations altered the plastic response exhibited by the wild-type allele. Comparing the effects of these mutations with the effects of 30 P_TDH3 polymorphisms on expression plasticity in the same environments provided evidence of natural selection acting to prevent the plastic response in P_TDH3 activity between glucose and galactose from becoming larger. The largest changes in expression plasticity were observed between fermentable (glucose or galactose) and nonfermentable (glycerol) carbon sources and were caused by mutations located in the RAP1 and GCR1 transcription factor binding sites. Mutations altered expression plasticity most frequently between the two fermentable environments, with mutations causing significant changes in plasticity between glucose and galactose distributed throughout the promoter, suggesting they might affect chromatin structure. Taken together, these results provide insight into the molecular mechanisms underlying gene-by-environment interactions affecting gene expression as well as the evolutionary dynamics affecting natural variation in plasticity of gene expression.

The effect of induced mutations on quantitative traits in Arabidopsis thaliana: Natural versus artificial conditions

Mutations are the ultimate source of all genetic variations. New mutations are expected to affect quantitative traits differently depending on the extent to which traits contribute to fitness and the environment in which they are tested. The dogma is that the preponderance of mutations affecting fitness will be skewed toward deleterious while their effects on nonfitness traits will be bidirectionally distributed. There are mixed views on the role of stress in modulating these effects. We quantify mutation effects by inducing mutations in Arabidopsis thaliana (Columbia accession) using the chemical ethylmethane sulfonate. We measured the effects of new mutations relative to a premutation founder for fitness components under both natural (field) and artificial (growth room) conditions. Additionally, we measured three other quantitative traits, not expected to contribute directly to fitness, under artificial conditions. We found that induced mutations were equally as likely to increase as decrease a trait when that trait was not closely related to fitness (traits that were neither survivorship nor reproduction). We also found that new mutations were more likely to decrease fitness or fitness‐related traits under more stressful field conditions than under relatively benign artificial conditions. In the benign condition, the effect of new mutations on fitness components was similar to traits not as closely related to fitness. These results highlight the importance of measuring the effects of new mutations on fitness and other traits under a range of conditions.

Fitness Effects of Spontaneous Mutations in Picoeukaryotic Marine Green Algae

Estimates of the fitness effects of spontaneous mutations are important for understanding the adaptive potential of species. Here, we present the results of mutation accumulation experiments over 265–512 sequential generations in four species of marine unicellular green algae, Ostreococcus tauri RCC4221, Ostreococcus mediterraneus RCC2590, Micromonas pusilla RCC299, and Bathycoccus prasinos RCC1105. Cell division rates, taken as a proxy for fitness, systematically decline over the course of the experiment in O. tauri, but not in the three other species where the MA experiments were carried out over a smaller number of generations. However, evidence of mutation accumulation in 24 MA lines arises when they are exposed to stressful conditions, such as changes in osmolarity or exposure to herbicides. The selection coefficients, estimated from the number of cell divisions/day, varies significantly between the different environmental conditions tested in MA lines, providing evidence for advantageous and deleterious effects of spontaneous mutations. This suggests a common environmental dependence of the fitness effects of mutations and allows the minimum mutation/genome/generation rates to be inferred at 0.0037 in these species.

The fitness effects of a point mutation in Escherichia coli change with founding population density

Although intraspecific competition plays a seminal role in organismal evolution, little is known about the fitness effects of mutations at different population densities. We identified a point mutation in the cyclic AMP receptor protein (CRP) gene in Escherichia coli that confers significantly higher fitness than the wildtype at low founding population density, but significantly lower fitness at high founding density. Because CRP is a transcription factor that regulates the expression of nearly 500 genes, we compared global gene expression profiles of the mutant and wildtype strains. This mutation (S63F) does not affect expression of crp itself, but it does significantly affect expression of 170 and 157 genes at high and low founding density, respectively. Interestingly, acid resistance genes, some of which are known to exhibit density-dependent effects in E. coli, were consistently differentially expressed at high but not low density. As such, these genes may play a key role in reducing the crp mutant's fitness at high density, although other differentially expressed genes almost certainly also contribute to the fluctuating fitness differences we observed. Whatever the causes, we suspect that many mutations may exhibit density-dependent fitness effects in natural populations, so the fate of new mutations may frequently depend on the effective population size when they originate.

Field measurements of genotype by environment interaction for fitness caused by spontaneous mutations in Arabidopsis thaliana

As the ultimate source of genetic diversity, spontaneous mutation is critical to the evolutionary process. The fitness effects of spontaneous mutations are almost always studied under controlled laboratory conditions rather than under the evolutionarily relevant conditions of the field. Of particular interest is the conditionality of new mutations-that is, is a new mutation harmful regardless of the environment in which it is found? In other words, what is the extent of genotype-environment interaction for spontaneous mutations? We studied the fitness effects of 25 generations of accumulated spontaneous mutations in Arabidopsis thaliana in two geographically widely separated field environments, in Michigan and Virginia. At both sites, mean total fitness of mutation accumulation lines exceeded that of the ancestors, contrary to the expected decrease in the mean due to new mutations but in accord with prior work on these MA lines. We observed genotype-environment interactions in the fitness effects of new mutations, such that the effects of mutations in Michigan were a poor predictor of their effects in Virginia and vice versa. In particular, mutational variance for fitness was much larger in Virginia compared to Michigan. This strong genotype-environment interaction would increase the amount of genetic variation maintained by mutation-selection balance.

The phenotypic effects of spontaneous mutations in different environments

Understanding the context dependence of mutation represents the current frontier of mutation research. In particular, understanding how traits vary in their abilities to accrue mutational variation and how the environment influences expression of mutant phenotypes yields insight into evolutionary processes. We conducted phenotypic assays in four environments using a set of Daphnia pulex mutation accumulation lines to examine the context dependence of mutation. Life-history traits accrued mutational variance faster than morphological traits when considered in individual environments. Across environments, the mutational variance in plasticity was also greater for life-history traits than for morphological traits, although this pattern was less robust. In addition, the expression of mutational variance depended on the environment, which resulted in changes in the rank order of genotype performance across environments in some cases. Such cryptic genetic variation resulting from mutation may maintain genetic diversity and allow for rapid adaptation in spatially or temporally variable environments.

Mutation studies in ascidians: a review

Historically, mutations have had a significant impact on the study of developmental processes and phenotypic evolution. Lesions in DNA are created by artificial methods or detected by natural genetic variation. Random mutations are then ascribed to genetic change by direct sequencing or positional cloning. Tunicate species of the ascidian genus Ciona represent nearly fully realized model systems in which gene function can be investigated in depth. Additionally, tunicates are valuable organisms for the study of naturally occurring mutations due to the capability to exploit genetic variation down to the molecular level. Here, we summarize the available information about how mutations are studied in ascidians with examples of insights that have resulted from these applications. We also describe notions and methodologies that might be useful for the implementation of easy and tight procedures for mutations studies in Ciona.

The contribution of spontaneous mutations to thermal sensitivity curve variation in Drosophila serrata

Many traits studied in ecology and evolutionary biology change their expression in response to a continuously varying environmental factor. One well-studied example are thermal performance curves (TPCs); continuous reaction norms that describe the relationship between organismal performance and temperature and are useful for understanding the trade-offs involved in thermal adaptation. We characterized curves describing the thermal sensitivity of voluntary locomotor activity in a set of 66 spontaneous mutation accumulation lines in the fly Drosophila serrata. Factor-analytic modeling of the mutational variance-covariance matrix, M, revealed support for three axes of mutational variation in males and two in females. These independent axes of mutational variance corresponded well to the major axes of TPC variation required for different types of thermal adaptation; "faster-slower" representing changes in performance largely independent of temperature, and the "hotter-colder" and "generalist-specialist" axes, representing trade-offs. In contrast to its near-absence from standing variance in this species, a "faster-slower" axis, accounted for most mutational variance (75% in males and 66% in females) suggesting selection may easily fix or remove these types of mutations in outbred populations. Axes resembling the "hotter-colder" and "generalist-specialist" modes of variation contributed less mutational variance but nonetheless point to an appreciable input of new mutations that may contribute to thermal adaptation.

Field-based insights to the evolution of specialization: plasticity and fitness across habitats in a specialist/generalist species pair

Factors promoting the evolution of specialists versus generalists have been little studied in ecological context. In a large-scale comparative field experiment, we studied genotypes from naturally evolved populations of a closely related generalist/specialist species pair (Polygonum persicaria and P. hydropiper), reciprocally transplanting replicates of multiple lines into open and partially shaded sites where the species naturally co-occur. We measured relative fitness, individual plasticity, herbivory, and genetic variance expressed in the contrasting light habitats at both low and high densities. Fitness data confirmed that the putative specialist out-performed the generalist in only one environment, the favorable full sun/low-density environment to which it is largely restricted in nature, while the generalist had higher lifetime reproduction in both canopy and dense neighbor shade. The generalist, P. persicaria, also expressed greater adaptive plasticity for biomass allocation and leaf size in shaded conditions than the specialist. We found no evidence that the ecological specialization of P. hydropiper reflects either genetically based fitness trade-offs or maintenance costs of plasticity, two types of genetic constraint often invoked to prevent the evolution of broadly adaptive genotypes. However, the patterns of fitness variance and herbivore damage revealed how release from herbivory in a new range can cause an introduced species to evolve as a specialist in that range, a surprising finding with important implications for invasion biology. Patterns of fitness variance between and within sites are also consistent with a possible role for the process of mutation accumulation (in this case, mutations affecting shade-expressed phenotypes) in the evolution and/or maintenance of specialization in P. hydropiper.

Fitness of Arabidopsis thaliana mutation accumulation lines whose spontaneous mutations are known

Despite the fundamental importance of mutation to the evolutionary process, we have little knowledge of the direct consequences of specific spontaneous mutations to the fitness of the organism. Combining results of whole-genome sequencing with repeated field assays of survival and reproduction, we quantify the combined effects on fitness of spontaneous mutations identified in Arabidopsis thaliana. We demonstrate that the effects are beneficial, deleterious, or neutral depending on the environmental context. Some lines, bearing mutations disrupting known loci, differ strongly in fitness from the founder or premutation genotype. Those effects vary across environments, for example, a line with a major deletion spanning a transcription factor gene expressed lower fitness than the founder under most conditions but exceeded the founder's fitness in one environment. The large contribution of genotype by environment interaction (G × E) to mutation effects on fitness implies spatial and/or temporal variation in selection on new mutations and could contribute to the maintenance of standing genetic variation.

Spontaneous mutation parameters for Arabidopsis thaliana measured in the wild

Mutations are the ultimate source of genetic diversity and their contributions to evolutionary process depend critically on their rate and their effects on traits, notably fitness. Mutation rate and mutation effect can be measured simultaneously through the use of mutation accumulation lines, and previous mutation accumulation studies measuring these parameters have been performed in laboratory conditions. However, estimation of mutation parameters for fitness in wild populations requires assays in environments where mutations are exposed to natural selection and natural environmental variation. Here we quantify mutation parameters in both the wild and greenhouse environments using 100 25th generation Arabidopsis thaliana mutation accumulation lines. We found significantly greater mutational variance and a higher mutation rate for fitness under field conditions relative to greenhouse conditions. However, our field estimates were low when scaled to natural environmental variation. Many of the mutation accumulation lines have increased fitness, counter to the expectation that nearly all mutations decrease fitness. A high mutation rate and a low mutational contribution to phenotypic variation may explain observed levels of natural genetic variation. Our findings indicate that mutation parameters are not fixed, but are variables whose values may reflect the specific environment in which mutations are tested.

Cumulative effects of spontaneous mutations for fitness in Caenorhabditis: role of genotype, environment and stress

It is often assumed that the mutation rate is an evolutionarily optimized property of a taxon. The relevant mutation rate is for mutations that affect fitness, U, but the strength of selection on the mutation rate depends on the average effect of a mutation. Determination of U is complicated by the possibility that mutational effects depend on the particular environmental context in which the organism exists. It has been suggested that the effects of deleterious mutations are typically magnified in stressful environments, but most studies confound genotype with environment, so it is unclear to what extent environmental specificity of mutations is specific to a particular starting genotype. We report a study designed to separate effects of species, genotype, and environment on the degradation of fitness resulting from new mutations. Mutations accumulated for >200 generations at 20 degrees in two strains of two species of nematodes that differ in thermal sensitivity. Caenorhabditis briggsae and C. elegans have similar demography at 20 degrees, but C. elegans suffers markedly reduced fitness at 25 degrees. We find little evidence that mutational properties differ depending on environmental conditions and mutational correlations between environments are close to those expected if effects were identical in both environments.

Evolution in heterogeneous environments and the potential of maintenance of genetic variation in traits of adaptive significance

The maintenance of genetic variation in traits of adaptive significance has been a major dilemma of evolutionary biology. Considering the pattern of increased genetic variation associated with environmental clines and heterogeneous environments, selection in heterogeneous environments has been proposed to facilitate the maintenance of genetic variation. Some models examining whether genetic variation can be maintained, in heterogeneous environments are reviewed. Genetic mechanisms that constrain evolution in quantitative genetic traits indicate that genetic variation can be maintained but when is not clear. Furthermore, no comprehensive models have been developed, likely due to the genetic and environmental complexity of this issue. Therefore, I have suggested two empirical approaches to provide insight for future theoretical and empirical research. Traditional path analysis has been a very powerful approach for understanding phenotypic selection. However, it requires substantial information on the biology of the study system to construct a causal model and alternatives. Exploratory path analysis is a data driven approach that uses the statistical relationships in the data to construct a set of models. For example, it can be used for understanding phenotypic selection in different environments, where there is no prior information to develop path models in the different environments. Data from Brassica rapa grown in different nutrients indicated that selection changed in the different environments. Experimental evolutionary studies will provide direct tests as to when genetic variation is maintained.