Increase of the spontaneous mutation rate in a long-term experiment with Drosophila melanogaster

In a previous experiment, the effect of 255 generations of mutation accumulation (MA) on the second chromosome viability of Drosophila melanogaster was studied using 200 full-sib MA1 lines and a large C1 control, both derived from a genetically homogeneous base population. At generation 265, one of those MA1 lines was expanded to start 150 new full-sib MA2 lines and a new C2 large control. After 46 generations, the rate of decline in mean viability in MA2 was approximately 2.5 times that estimated in MA1, while the average degree of dominance of mutations was small and nonsignificant by generation 40 and moderate by generation 80. In parallel, the inbreeding depression rate for viability and the amount of additive variance for two bristle traits in C2 were 2-3 times larger than those in C1. The results are consistent with a mutation rate in the line from which MA2 and C2 were derived about 2.5 times larger than that in MA1. The mean viability of C2 remained roughly similar to that of C1, but the rate of MA2 line extinction increased progressively, leading to mutational collapse, which can be ascribed to accelerated mutation and/or synergy after important deleterious accumulation.     

The rate of mutation and the homozygous and heterozygous mutational effects for competitive viability: a long-term experiment with Drosophila melanogaster

The effect of 250 generations of mutation accumulation (MA) on the second chromosome competitive viability of Drosophila melanogaster was analyzed both in homozygous and heterozygous conditions. We used full-sib MA lines, where selection hampers the accumulation of severely deleterious mutations but is ineffective against mildly deleterious ones. A large control population was simultaneously evaluated. Competitive viability scores, unaffected by the expression of mutations in heterozygosis, were obtained relative to a Cy/L(2) genotype. The rate of decline in mean DeltaM approximately 0.1% was small. However, that of increase in variance DeltaV approximately 0.08 x 10(-3) was similar to the values obtained in previous experiments when severely deleterious mutations were excluded. The corresponding estimates of the mutation rate lambda > or = 0.01 and the average effect of mutations E(s) < or = 0.08 are in good agreement with Bateman-Mukai and minimum distance estimates for noncompetitive viability obtained from the same MA lines after 105 generations. Thus, competitive and noncompetitive viability show similar mutational properties. The regression estimate of the degree of dominance for mild-to-moderate deleterious mutations was approximately 0.3, suggesting that the pertinent value for new unselected mutations should be somewhat smaller.     

Effectiveness of sexual selection in preventing fitness deterioration in bulb mite populations under relaxed natural selection

Under the 'good genes' mechanism of sexual selection (SS), females benefit from mate choice indirectly: their offspring inherit genes of the preferred, high quality fathers. Recent models assume that the genetic variance for male quality is maintained by deleterious mutations. Consequently, SS can be predicted to remove deleterious mutations from populations. We tested this prediction by relaxing selection in populations of the bulb mite, thus increasing their rate of accumulation of deleterious mutation. SS, allowed to operate in half of these populations, did not prevent the fitness decline observed in the other half of the relaxed selection lines. After 11 generations of relaxed selection, female fecundity in lines in which males were allowed to compete for females declined compared with control populations by similar amount as in monogamous lines (17.5 and 14.5%, respectively), whereas other fitness components (viability, longevity, male reproductive success) did not differ significantly between both types of lines and control populations.     

Fitness decline in spontaneous mutation accumulation lines of Caenorhabditis elegans with varying effective population sizes

The rate and fitness effects of new mutations have been investigated by mutation accumulation (MA) experiments in which organisms are maintained at a constant minimal population size to facilitate the accumulation of mutations with minimal efficacy of selection. We evolved 35 MA lines of Caenorhabditis elegans in parallel for 409 generations at three population sizes (N = 1, 10, and 100), representing the first spontaneous long-term MA experiment at varying population sizes with corresponding differences in the efficacy of selection. Productivity and survivorship in the N = 1 lines declined by 44% and 12%, respectively. The average effects of deleterious mutations in N = 1 lines are estimated to be 16.4% for productivity and 11.8% for survivorship. Larger populations (N = 10 and 100) did not suffer a significant decline in fitness traits despite a lengthy and sustained regime of consecutive bottlenecks exceeding 400 generations. Together, these results suggest that fitness decline in very small populations is dominated by mutations with large deleterious effects. It is possible that the MA lines at larger population sizes contain a load of cryptic deleterious mutations of small to moderate effects that would be revealed in more challenging environments.     

A Pleiotropic Nonadditive Model of Variation in Quantitative Traits

A model of mutation-selection-drift balance incorporating pleiotropic and dominance effects of new mutations on quantitative traits and fitness is investigated and used to predict the amount and nature of genetic variation maintained in segregating populations. The model is based on recent information on the joint distribution of mutant effects on bristle traits and fitness in Drosophila melanogaster from experiments on the accumulation of spontaneous and P element-induced mutations. These experiments suggest a leptokurtic distribution of effects with an intermediate correlation between effects on the trait and fitness. Mutants of large effect tend to be partially recessive while those with smaller effect are on average additive, but apparently with very variable gene action. The model is parameterized with two different sets of information derived from P element insertion and spontaneous mutation data, though the latter are not fully known. They differ in the number of mutations per generation which is assumed to affect the trait. Predictions of the variance maintained for bristle number assuming parameters derived from effects of P element insertions, in which the proportion of mutations with an effect on the trait is small, fit reasonably well with experimental observations. The equilibrium genetic variance is nearly independent of the degree of dominance of new mutations. Heritabilities of between 0.4 and 0.6 are predicted with population sizes from 10(4) to 10(6), and most of the variance for the metric trait in segregating populations is due to a small proportion of mutations (about 1% of the total number) with neutral or nearly neutral effects on fitness and intermediate effects on the trait (0.1-0.5σ(P)). Much of the genetic variance is contributed by recessive or partially recessive mutants, but only a small proportion (about 10%) of the genetic variance is dominance variance. The amount of apparent selection on the trait itself generated by the model is very small. If a model is assumed in which all mutation events have an effect on the quantitative trait, the majority of the genetic variance is contributed by deleterious mutations with tiny effects on the trait. If such a model is assumed for viability, the heritability is about 0.1, independent of the population size.     

On the rate and linearity of viability declines in Drosophila mutation-accumulation experiments: genomic mutation rates and synergistic epistasis revisited

High rates of deleterious mutations could severely reduce the fitness of populations, even endangering their persistence; these effects would be mitigated if mutations synergize each others' effects. An experiment by Mukai in the 1960s gave evidence that in Drosophila melanogaster, viability-depressing mutations occur at the surprisingly high rate of around one per zygote and that the mutations interact synergistically. A later experiment by Ohnishi seemed to support the high mutation rate, but gave no evidence for synergistic epistasis. Both of these studies, however, were flawed by the lack of suitable controls for assessing viability declines of the mutation-accumulation (MA) lines. By comparing homozygous viability of the MA lines to simultaneously estimated heterozygous viability and using estimates of the dominance of mutations in the experiments, I estimate the viability declines relative to an appropriate control. This approach yields two unexpected conclusions. First, in Ohnishi's experiment as well as in Mukai's, MA lines showed faster-than-linear declines in viability, indicative of synergistic epistasis. Second, while Mukai's estimate of the genomic mutation rate is supported, that from Ohnishi's experiment is an order of magnitude lower. The different results of the experiments most likely resulted from differences in the starting genotypes; even within Mukai's experiment, a subset of MA lines, which I argue probably resulted from a contamination event, showed much slower viability declines than did the majority of lines. Because different genotypes may show very different mutational behavior, only studies using many founding genotypes can determine the average rate and distribution of effects of mutations relevant to natural populations.     

The effects of spontaneous mutation on competitive fitness in Drosophila melanogaster

Abstract We have analysed the effect of 288 generations of mutation accumulation (MA) on chromosome II competitive fitness in 21 full‐sib lines of Drosophila melanogaster and in a large control population, all derived from the same isogenic base. The rate of mean log‐fitness decline and that of increase of the between‐line variance were consistent with a low rate (λ ≈ 0.03 per gamete and generation), and moderate average fitness effect [E(s) ≈ 0.1] of deleterious mutation. Subsequently, crosses were made between pairs of MA lines, and these were maintained with effective size on the order of a few tens. In these crosses, MA recombinant chromosomes quickly recovered to about the average fitness level of control chromosomes. Thus, deleterious mutations responsible for the fitness decline were efficiently selected against in relatively small populations, confirming that their effects were larger than a few percent.     

Spontaneous mutations in diploid Saccharomyces cerevisiae: more beneficial than expected

We performed a 1012-generation mutation-accumulation (MA) experiment in the yeast, Saccharomyces cerevisiae. The MA lines exhibited a significant reduction in mean fitness and a significant increase in variance in fitness. We found that 5.75% of the fitness-altering mutations accumulated were beneficial. This finding contradicts the widely held belief that nearly all fitness-altering mutations are deleterious. The mutation rate was estimated as 6.3 x 10(-5) mutations per haploid genome per generation and the average heterozygous fitness effect of a mutation as 0.061. These estimates are compatible with previous estimates in yeast.     

Rapid mutational declines of viability in Drosophila

High rates of mildly deleterious mutation could cause the extinction of small populations, reduce neutral genetic variation and provide an evolutionary advantage for sex. In the first attempts to estimate the rate of mildly deleterious mutation, Mukai and Ohnishi allowed spontaneous mutations to accumulate on D. melanogaster second chromosomes shielded from recombination and selection. Viability of the shielded chromosomes appeared to decline rapidly, implying a deleterious mutation rate on the order of one per zygote per generation. These results have been challenged, however; at issue is whether Mukai and Ohnishi may have confounded viability declines caused by mutation with declines resulting from environmental changes or other extraneous factors. Here, using a method not sensitive to non-mutational viability changes, I reanalyse the previous mutation-accumulation (MA) experiments, and report the results of a new one. I show that in each of four experiments, including Mukai's two experiments, viability declines due to mildly deleterious mutations were rapid. The results give no support for the view that Mukai overestimated the declines. Although there is substantial variation in estimates of genomic mutation rates from the experiments, this variation is probably due to some combination of sampling error, strain differences and differences in assay conditions, rather than to failure to distinguish mutational and non-mutational viability changes.     

POLYGENIC MUTATION IN DROSOPHILA MELANOGASTER: ESTIMATES FROM DIVERGENCE AMONG INBRED STRAINS

A highly inbred line of Drosophila melanogaster was subdivided into 25 replicate sublines, which were independently maintained for 100 generations with 10 pairs of unselected flies per generation. The polygenic mutation rate (V_M) for two quantitative traits, abdominal and sternopleural bristle number, was estimated from divergence among sublines at 10 generation intervals from generations 30-100, and from response of each line to divergent selection after more than 65 generations of mutation accumulation. Estimates of V_M averaged over males and females both from divergence among lines and from response to selection within lines were 3.3 × 10^-3 V_E for abdominal bristles and 1.5 × 10^-3 V_E for sternopleural bristles, where V_E is the environmental variance. The actual rate of production of mutations affecting these traits may be considerably higher if the traits are under stabilizing selection, and if mutations affecting bristle number have deleterious effects on fitness. There was a substantial component of variance for sex × mutant effect interaction and the sublines evolved highly significant mutational variation in sex dimorphism of abdominal bristle number. Pleiotropic effects on sex dimorphism may be a general property of mutations at loci determining bristle number.     

Deleterious mutation in related species of the plant genus Amsinckia with contrasting mating systems

Theory for the evolution of modifiers of the rate of mutation suggests that a lower rate of mutation may evolve after the breakdown of mechanisms that enforce outcrossing. Mutation accumulation (MA) experiments were conducted to compare deleterious mutation parameters in two closely related species of the plant genus Amsinckia, a group that exhibits wide variation in the mating system. One of the two species studied (A. douglasiana) is predominantly outcrossed in natural populations, where as the other species (A. gloriosa) is predominantly self-pollinated. Progeny assays of flower number per plant from generation 1 lines (control) and generation 11 lines (MA treatment) were conducted in both species. Dry weight measurements of progeny from the control and MA treatment in A. douglasiana also were made. Estimation of mutation parameters was conducted using maximum likelihood under the assumption of a gamma distribution of mutational effects. The two species exhibited similar rates and effects of deleterious mutation affecting flower number. Estimates of mutation rate for dry weight in A. douglasiana are close to those for flower number. Overall, the estimates of mutation parameters observed in these species are intermediate within the range reported for fitness components in other eukaryotes. The results are discussed within the context of evolutionary change in deleterious mutation accompanying mating system evolution and with respect to previous estimates of mutation parameters based on assays of inbreeding depression and the assumption of mutation-selection equilibrium.     

Abiotic stress does not magnify the deleterious effects of spontaneous mutations

Although the effects of deleterious alleles often are predicted to be greater in stressful environments, there is no theoretical basis for this prediction and the empirical evidence is mixed. Here we characterized the effects of three types of abiotic stress (thermal, oxidative and hyperosmotic) on two sets of nematode (Caenorhabditis elegans) mutation accumulation (MA) lines that differ by threefold in fitness. We compared the survival and egg-to-adult viability between environments (benign and stressful) and between fitness categories (high-fitness MA, low-fitness MA). If the environment and mutation load have synergistic effects on trait means, then the difference between the high and low-fitness MA lines should be larger in stressful environments. Although the stress treatments consistently decreased survival and/or viability, we did not detect significant interactions between fitness categories and environment types. In contrast, we did find consistent evidence for synergistic effects on (micro)environmental variation. The lack of signal in trait means likely reflects the very low starting fitness of some low-fitness MA lines, the potential for cross-stress responses and the context dependence of mutational effects. In addition, the large increases in the environmental variance in the stressful environments may have masked small changes in trait means. These results do not provide evidence for synergism between mutation and stress.     

Selection on viability of individuals heterozygous for the temperature-sensitive lethal mutation l(2)M167(DTS) in experimental populations of Drosophila melanogaster

In experiments on introduction of mutation l(2)M167(DTS) in Drosophila melanogaster populations, larval and pupal viability and developmental rate are limiting factors determining the intensity of selection on the l(2)M167(DTS) mutation. Notwithstanding the rapid elimination of the mutation from the population, positive selection for viability was shown, which increased fitness of the mutation carriers in generations. The fitness component viability was estimated in individuals l(2)M167(DTS)/+; relative to that of wild-type individuals, it varied from 0.1 to 1. Factors affecting this trait in overcrowded populations were found.     

RAPID DECLINE IN FITNESS OF MUTATION ACCUMULATION LINES OF GONOCHORISTIC (OUTCROSSING) CAENORHABDITIS NEMATODES

Evolutionary theory predicts that the strength of natural selection to reduce the mutation rate should be stronger in self‐fertilizing than in outcrossing taxa. However, the relative efficacy of selection on mutation rate relative to the many other factors influencing the evolution of any species is poorly understood. To address this question, we allowed mutations to accumulate for ∼100 generations in several sets of “mutation accumulation” (MA) lines in three species of gonochoristic (dieocious) Caenorhabditis (C. remanei, C. brenneri, C. sp. 5) as well as in a dioecious strain of the historically self‐fertile hermaprohodite C. elegans. In every case, the rate of mutational decay is substantially greater in the gonochoristic taxa than in C. elegans (∼4× greater on average). Residual heterozygosity in the ancestral controls of these MA lines introduces some complications in interpreting the results, but circumstantial evidence suggests the results are not primarily due to inbreeding depression resulting from residual segregating variation. The results suggest that natural selection operates to optimize the mutation rate in Caenorhabditis and that the strength (or efficiency) of selection differs consistently on the basis of mating system, as predicted by theory. However, context‐dependent environmental and/or synergistic epistasis could also explain the results.     

Polygenic Mutation in Drosophila Melanogaster: Estimates from Response to Selection of Inbred Strains

Replicated divergent artificial selection for abdominal and sternopleural bristle number from a highly inbred strain of Drosophila melanogaster resulted in an average divergence after 125 generations of selection of 12.0 abdominal and 8.2 sternopleural bristles from the accumulation of new mutations affecting bristle number. Responses to selection were highly asymmetrical, with greater responses for low abdominal and high sternopleural bristle numbers. Estimates of V(M), the mutational variance arising per generation, based on the infinitesimal model and averaged over the responses to the first 25 generations of selection, were 4.32 X 10(-3) V(E) for abdominal bristle number and 3.66 X 10(-3) V(E) for sternopleural bristle number, where V(E) is the environmental variance. Based on 10 generations of divergent selection within lines from generation 93, V(M) for abdominal bristle number was 6.75 X 10(-3) V(E) and for sternopleural bristle number was 5.31 X 10(-3) V(E). However, estimates of V(M) using the entire 125 generations of response to selection were lower and generally did not fit the infinitesimal model largely because the observed decelerating responses were not compatible with the predicted increasing genetic variance over time. These decelerating responses, periods of response in the opposite direction to artificial selection, and rapid responses to reverse selection all suggest new mutations affecting bristle number on average have deleterious effects on fitness. Commonly observed periods of accelerated responses followed by long periods of stasis suggest a leptokurtic distribution of mutational effects for bristles.     

Polygenic Mutation in Drosophila Melanogaster: The Causal Relationship of Bristle Number to Fitness

The association between sternopleural and abdominal bristle number and fitness in Drosophila melanogaster was determined for sublines of an initially highly inbred strain that were maintained by divergent artificial selection for 150 generations or by random mating for 180 generations. Replicate selection lines had more extreme bristle numbers than those that were maintained without artificial selection at the same census size for approximately the same number of generations. The average fitness, estimated by a single generation of competition against a compound autosome strain, was 0.17 for lines selected for high and low abdominal bristle numbers and 0.19 for lines selected for high and low sternopleural bristle number. The average fitness of unselected lines, 0.46, was significantly higher than that of the selection lines. The fitnesses and the relationships of bristle number to fitness in progeny of all possible crosses of high X high (H X H), high X low (H X L) and low X low (L X L) selection lines were examined to determine whether the observed intermediate optima were caused by direct stabilizing selection on bristle number or by apparent stabilizing selection mediated through deleterious pleiotropic fitness effects of mutations affecting bristle number. Although bristle number was nearly additive for progeny of H X H, H X L and L X L crosses among sternopleural bristle selection lines, their mean fitnesses were not significantly different from each other, or from the mean fitness of the unselected lines, suggesting partly or completely recessive pleiotropic fitness effects cause apparent stabilizing selection. The average fitness of the progeny of H X H abdominal bristle selection lines was not significantly different from the fitness of unselected lines, but the mean fitness of the progeny of L X L crosses was not significantly different from that of the pure low lines. This is consistent with direct selection against low but not high abdominal bristle number, but the interpretation is confounded by variation in average degree of dominance for fitness (on average recessive in the high abdominal bristle selection lines and additive in the low abdominal bristle selection lines). Neither direct stabilizing selection nor pleiotropy, therefore, can account for all the observations.     

Sexual selection on spontaneous mutations strengthens the between‐sex genetic correlation for fitness

A proposed benefit to sexual selection is that it promotes purging of deleterious mutations from populations. For this benefit to be realized, sexual selection, which is usually stronger on males, must purge mutations deleterious to both sexes. Here, we experimentally test the hypothesis that sexual selection on males purges deleterious mutations that affect both male and female fitness. We measured male and female fitness in two panels of spontaneous mutation‐accumulation lines of the fly, Drosophila serrata, each established from a common ancestor. One panel of mutation accumulation lines limited both natural and sexual selection (LS lines), whereas the other panel limited natural selection, but allowed sexual selection to operate (SS lines). Although mutation accumulation caused a significant reduction in male and female fitness in both the LS and SS lines, sexual selection had no detectable effect on the extent of the fitness reduction. Similarly, despite evidence of mutational variance for fitness in males and females of both treatments, sexual selection had no significant impact on the amount of mutational genetic variance for fitness. However, sexual selection did reshape the between‐sex correlation for fitness: significantly strengthening it in the SS lines. After 25 generations, the between‐sex correlation for fitness was positive but considerably less than one in the LS lines, suggesting that, although most mutations had sexually concordant fitness effects, sex‐limited, and/or sex‐biased mutations contributed substantially to the mutational variance. In the SS lines this correlation was strong and could not be distinguished from unity. Individual‐based simulations that mimick the experimental setup reveal two conditions that may drive our results: (1) a modest‐to‐large fraction of mutations have sex‐limited (or highly sex‐biased) fitness effects, and (2) the average fitness effect of sex‐limited mutations is larger than the average fitness effect of mutations that affect both sexes similarly.     

Polygenic Mutation in Drosophila Melanogaster: Non-Linear Divergence among Unselected Strains

A highly inbred strain of Drosophila melanogaster was subdivided into 20 replicate sublines that were maintained independently with 10 pairs of randomly sampled parents per generation for 180 generations. The variance between lines in abdominal and sternopleural bristle number increased little after 100 generations, in contrast to the neutral expectation of a linear increase; and the covariances of line means between different generations declined with increasing number of generations apart, in contrast to the neutral expectation of constant covariance. Thus, under a neutral model, the estimates of mutational variance were lower than for previous estimates from the first 100 generations of subline divergence. An autoregressive model was fitted to the variance of line means that indicated strong natural selection. There is no single unequivocal explanation for the results. Possible and nonexclusive alternatives include stabilizing selection on bristle number and deleterious effects on fitness of bristle mutations. The inferred strengths of selection on both traits are too high for stabilizing selection alone, and the between-line variance did not continue to increase sufficiently for pleiotropy alone to account for the observations. A third potential explanation that does not invoke selection is duplicate epistasis between mutations affecting bristle number.     

Genomic mutation in lines of Arabidopsis thaliana exposed to ultraviolet-B radiation

Studies that have attempted to estimate the rate of deleterious mutation have typically been conducted under low levels of ultraviolet-B (UV-B) radiation, a naturally occurring mutagen. We conducted experiments to test whether the inclusion of natural levels of UV-B radiation in mutation-accumulation (MA) experiments influences the rate and effects of mildly deleterious mutation in the plant Arabidopsis thaliana. Ten generations of MA proved insufficient to observe significant changes in means or among-line variances in experimental lines maintained either with or without supplemental UV-B radiation. Maximum-likelihood estimates of mutation rate for total flower number revealed a small but significant rate of mutation for MA lines propagated under supplemental UV-B exposure, but not for those in which supplemental UV-B was omitted. A fraction of the flower number mutations under UV-B (approximately 25-30%) are estimated to increase flower number. Results from the application of transposon display to plant materials obtained after MA, in both the presence and absence of supplemental UV-B, suggest that the average rate of transposition for the class I and II transposable elements (TEs) surveyed was no more than 10(-4). Overall, the estimates of mutation parameters are qualitatively similar to what has been observed in other MA experiments with this species in which supplemental UV-B levels have not been used. As well, it appears that naturally occurring levels of UV-B do not lead to detectable increases in levels of transposable element activity.     

The Genetic Structure of Natural Populations of DROSOPHILA MELANOGASTER. Xviii. Clinal and Uniform Genetic Variation over Populations

It has been reported in the previous papers of this series that in the eastern United States and Japan there is a north-to-south cline of additive genetic variance of viability and that the amount of the additive genetic variance in the northern population can be explained by mutation-selection balance. To determine whether or not the difference in the genetic variation in northern and southern populations can be explained by the differences in mutation rate and/or effective population size, numerical calculations were made using population genetic parameters. In addition, the average heterozygosities of the northern and southern populations at ten of 19 polymorphic structural loci surveyed were estimated in relation to the cline of additive genetic variance of viability, and the following findings were obtained. (1) The changes in mutation rate and population size cannot simultaneously explain the difference in additive genetic variance and inbreeding decline between the northern and southern populations. Thus, the operation of some kind of balancing selection, most likely diversifying selection, was suggested to explain the observed excess of additive genetic variance. (2) Estimates of the average heterozygosities of the southern population were not significantly different from those of the northern population. Thus, it was strongly suggested that the excess of additive genetic variance in the southern population cannot be caused by structural loci, but by factors outside the structural loci, and that protein polymorphisms are selectively neutral or nearly neutral.