Spontaneous mutational variances and covariances for fitness-related traits in Drosophila melanogaster

High and Highly Variable Spontaneous Mutation Rates in Daphnia

The rate and spectrum of spontaneous mutations are critical parameters in basic and applied biology because they dictate the pace and character of genetic variation introduced into populations, which is a prerequisite for evolution. We use a mutation–accumulation approach to estimate mutation parameters from whole-genome sequence data from multiple genotypes from multiple populations of Daphnia magna, an ecological and evolutionary model system. We report extremely high base substitution mutation rates (µ-n,bs = 8.96 × 10⁻⁹/bp/generation [95% CI: 6.66–11.97 × 10⁻⁹/bp/generation] in the nuclear genome and µ-m,bs = 8.7 × 10⁻⁷/bp/generation [95% CI: 4.40–15.12 × 10⁻⁷/bp/generation] in the mtDNA), the highest of any eukaryote examined using this approach. Levels of intraspecific variation based on the range of estimates from the nine genotypes collected from three populations (Finland, Germany, and Israel) span 1 and 3 orders of magnitude, respectively, resulting in up to a ∼300-fold difference in rates among genomic partitions within the same lineage. In contrast, mutation spectra exhibit very consistent patterns across genotypes and populations, suggesting the mechanisms underlying the mutational process may be similar, even when the rates at which they occur differ. We discuss the implications of high levels of intraspecific variation in rates, the importance of estimating gene conversion rates using a mutation–accumulation approach, and the interacting factors influencing the evolution of mutation parameters. Our findings deepen our knowledge about mutation and provide both challenges to and support for current theories aimed at explaining the evolution of the mutation rate, as a trait, across taxa.

Fitness and Genomic Consequences of Chronic Exposure to Low Levels of Copper and Nickel in Daphnia pulex Mutation Accumulation Lines

In at least some unicellular organisms, mutation rates are temporarily raised upon exposure to environmental stress, potentially contributing to the evolutionary response to stress. Whether this is true for multicellular organisms, however, has received little attention. This study investigated the effects of chronic mild stress, in the form of low-level copper and nickel exposure, on mutational processes in Daphnia pulex using a combination of mutation accumulation, whole genome sequencing and life-history assays. After over 100 generations of mutation accumulation, we found no effects of metal exposure on the rates of single nucleotide mutations and of loss of heterozygosity events, the two mutation classes that occurred in sufficient numbers to allow statistical analysis. Similarly, rates of decline in fitness, as measured by intrinsic rate of population increase and of body size at first reproduction, were negligibly affected by metal exposure. We can reject the possibility that Daphnia were insufficiently stressed to invoke genetic responses as we have previously shown rates of large-scale deletions and duplications are elevated under metal exposure in this experiment. Overall, the mutation accumulation lines did not significantly depart from initial values for phenotypic traits measured, indicating the lineage used was broadly mutationally robust. Taken together, these results indicate that the mutagenic effects of chronic low-level exposure to these metals are restricted to certain mutation classes and that fitness consequences are likely minor and therefore unlikely to be relevant in determining the evolutionary responses of populations exposed to these stressors.

Increase in viability due to the accumulation of X chromosome mutations in Drosophila melanogaster males

To increase our understanding of the role of new X-chromosome mutations in adaptive evolution, single-X Drosophila melanogaster males were mated with attached-X chromosome females, allowing the male X chromosome to accumulate mutations over 28 generations. Contrary to our hypothesis that male viability would decrease over time, due to the accumulation and expression of X-linked recessive deleterious mutations in hemizygous males, viability significantly increased. This increase may be attributed to germinal selection and to new X-linked beneficial or compensatory mutations, possibly supporting the faster-X hypothesis.

MORTALITY PLATEAUS AND THE EVOLUTION OF SENESCENCE: WHY ARE OLD-AGE MORTALITY RATES SO LOW?

Age-specific mortality rates level off far below 100% at advanced ages in experimental populations of Drosophila melanogaster and other organisms. This observation is inconsistent with the equilibrium predictions of both the antagonistic pleiotropy and mutation accumulation models of senescence, which, under a wide variety of assumptions, predict a "wall" of mortality rates near 100% at postreproductive ages. Previous models of age-specific mortality patterns are discussed in light of recent demographic data concerning late-age mortality deceleration and age-specific properties of new mutations. The most recent theory (Mueller and Rose 1996) argues that existing evolutionary models can easily and robustly explain the demographic data. Here we discuss the sensitivity of that analysis to different types of mutational effects, and demonstrate that its conclusion is very sensitive to assumptions about mutations. A legitimate resolution of evolutionary theory and demographic data will require experimental observations on the age-specificity of mutational effects for new mutations and the degree to which mortality rates in adjacent ages are constrained to be similar (positive pleiotropy), as well as consideration of redundancy and heterogeneity models from demographic theory.

SPONTANEOUS MUTATIONAL GENOTYPE-ENVIRONMENT INTERACTION FOR FITNESS-RELATED TRAITS IN DROSOPHILA MELANOGASTER

Spontaneous mutations were allowed to accumulate for 104-161 generations in 113-176 inbred lines, independently maintained by a single brother-sister mating per generation, all of them derived from a completely homozygous population of Drosophila melanogaster. In each of two to three consecutive generations, all lines were scored for fecundity, egg-to-pupa and pupa-to-adult viabilities, both in the standard laboratory culture medium (ST) and in three harsh media differing from the former by a single factor: higher temperature (HT), higher NaCl concentration (HSC), or a much reduced concentration of nutrients (D). Relative to the standard medium, productivity (fecundity × viability) decreased by 25% (HT), 66% (HSC), and 80% (D). In each medium, mutational variances of those traits and mutational covariances between all possible pairs were calculated from the between-line divergence (codivergence). Mutational correlations between character states in different media were also obtained. Because we used inbred lines, those estimates were mainly due to the accumulation of mildly detrimental mutations, deleterious mutations of large effect being underrepresented. For all traits, mutational heritabilities ranged from 1.41 × 10^-4 to 11.24 × 10^-4 , and did not increase with intensified environmental harshness. Mutational correlations between character states in different media were usually not large (average absolute value 0.31), reflecting a high degree of environmental specificity of the mutations involved. In our results, mutations quasi-neutral in ST conditions and mildly detrimental in more stressful media were not, as a class, important. Mutational correlations between fecundity and egg-to-pupa viability were small and positive in all media. Those involving pupa-to-adult viability were positive in HT, nonsignificant in HSC, and negative in ST and D, showing how the genetic covariance structure of quantitative traits in populations may change in variable environments.

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.

Spontaneous mutation accumulation in multiple strains of the green alga, Chlamydomonas reinhardtii

Estimates of mutational parameters, such as the average fitness effect of a new mutation and the rate at which new genetic variation for fitness is created by mutation, are important for the understanding of many biological processes. However, the causes of interspecific variation in mutational parameters and the extent to which they vary within species remain largely unknown. We maintained multiple strains of the unicellular eukaryote Chlamydomonas reinhardtii, for approximately 1000 generations under relaxed selection by transferring a single cell every ∼10 generations. Mean fitness of the lines tended to decline with generations of mutation accumulation whereas mutational variance increased. We did not find any evidence for differences among strains in any of the mutational parameters estimated. The overall change in mean fitness per cell division and rate of input of mutational variance per cell division were more similar to values observed in multicellular organisms than to those in other single-celled microbes. However, after taking into account differences in genome size among species, estimates from multicellular organisms and microbes, including our new estimates from C. reinhardtii, become substantially more similar. Thus, we suggest that variation in genome size is an important determinant of interspecific variation in mutational parameters.

The effect of spontaneous mutations on competitive ability

Understanding the impact of spontaneous mutations on fitness has many theoretical and practical applications in biology. Although mutational effects on individual morphological or life-history characters have been measured in several classic genetic model systems, there are few estimates of the rate of decline due to mutation for complex fitness traits. Here, we estimate the effects of mutation on competitive ability, an important complex fitness trait, in a model system for ecological and evolutionary genomics, Daphnia. Competition assays were performed to compare fitness between mutation-accumulation (MA) lines and control lines from eight different genotypes from two populations of Daphnia pulicaria after 30 and 65 generations of mutation accumulation. Our results show a fitness decline among MA lines relative to controls as expected, but highlight the influence of genomic background on this effect. In addition, in some assays, MA lines outperform controls providing insight into the frequency of beneficial mutations.

Purging deleterious mutations in conservation programmes: combining optimal contributions with inbred matings

Conservation programmes aim at minimising the loss of genetic diversity, which allows populations to adapt to potential environmental changes. This can be achieved by calculating how many offspring every individual should contribute to the next generation to minimise global coancestry. However, an undesired consequence of this strategy is that it maintains deleterious mutations, compromising the viability of the population. In order to avoid this, optimal contributions could be combined with inbred matings, to expose and eliminate recessive deleterious mutations by natural selection in a process known as purging. Although some populations that have undergone purging experienced reduced inbreeding depression, this effect is not consistent across species. Whether purging by inbred matings is efficient in conservation programmes depends on the balance between the loss of diversity, the initial decrease in fitness and the reduction in mutational load. Here we perform computer simulations to determine whether managing a population by combining optimal contributions with inbred matings improves its long-term viability while keeping reasonable levels of diversity. We compare the management based on genealogical information with management based on molecular data to calculate coancestries. In the scenarios analysed, inbred matings never led to higher fitness and usually maintained lower diversity than random or minimum coancestry matings. Replacing genealogical with molecular coancestry can maintain a larger genetic diversity but can also lead to a lower fitness. Our results are strongly dependent on the mutational model assumed for the trait under selection, the population size during management and the reproductive rate.

Joint allelic effects on fitness and metric traits

Theoretical explanations of empirically observed standing genetic variation, mutation, and selection suggest that many alleles must jointly affect fitness and metric traits. However, there are few direct demonstrations of the nature and extent of these pleiotropic associations. We implemented a mutation accumulation (MA) divergence experimental design in Drosophila serrata to segregate genetic variants for fitness and metric traits. By exploiting naturally occurring MA line extinctions as a measure of line-level total fitness, manipulating sexual selection, and measuring productivity we were able to demonstrate genetic covariance between fitness and standard metric traits, wing size, and shape. Larger size was associated with lower total fitness and male sexual fitness, but higher productivity. Multivariate wing shape traits, capturing major axes of wing shape variation among MA lines, evolved only in the absence of sexual selection, and to the greatest extent in lines that went extinct, indicating that mutations contributing wing shape variation also typically had deleterious effects on both total fitness and male sexual fitness. This pleiotropic covariance of metric traits with fitness will drive their evolution, and generate the appearance of selection on the metric traits even in the absence of a direct contribution to fitness.

Multivariate phenotypic divergence due to the fixation of beneficial mutations in experimentally evolved lineages of a filamentous fungus

The potential for evolutionary change is limited by the availability of genetic variation. Mutations are the ultimate source of new alleles, yet there have been few experimental investigations of the role of novel mutations in multivariate phenotypic evolution. Here, we evaluated the degree of multivariate phenotypic divergence observed in a long-term evolution experiment whereby replicate lineages of the filamentous fungus Aspergillus nidulans were derived from a single genotype and allowed to fix novel (beneficial) mutations while maintained at two different population sizes. We asked three fundamental questions regarding phenotypic divergence following approximately 800 generations of adaptation: (1) whether divergence was limited by mutational supply, (2) whether divergence proceeded in relatively many (few) multivariate directions, and (3) to what degree phenotypic divergence scaled with changes in fitness (i.e. adaptation). We found no evidence that mutational supply limited phenotypic divergence. Divergence also occurred in all possible phenotypic directions, implying that pleiotropy was either weak or sufficiently variable among new mutations so as not to constrain the direction of multivariate evolution. The degree of total phenotypic divergence from the common ancestor was positively correlated with the extent of adaptation. These results are discussed in the context of the evolution of complex phenotypes through the input of adaptive mutations.

Inbreeding-stress interactions: evolutionary and conservation consequences

The effect of environmental stress on the magnitude of inbreeding depression has a long history of intensive study. Inbreeding-stress interactions are of great importance to the viability of populations of conservation concern and have numerous evolutionary ramifications. However, such interactions are controversial. Several meta-analyses over the last decade, combined with omic studies, have provided considerable insight into the generality of inbreeding-stress interactions, its physiological basis, and have provided the foundation for future studies. In this review, we examine the genetic and physiological mechanisms proposed to explain why inbreeding-stress interactions occur. We specifically examine whether the increase in inbreeding depression with increasing stress could be due to a concomitant increase in phenotypic variation, using a larger data set than any previous study. Phenotypic variation does usually increase with stress, and this increase can explain some of the inbreeding-stress interaction, but it cannot explain all of it. Overall, research suggests that inbreeding-stress interactions can occur via multiple independent channels, though the relative contribution of each of the mechanisms is unknown. To better understand the causes and consequences of inbreeding-stress interactions in natural populations, future research should focus on elucidating the genetic architecture of such interactions and quantifying naturally occurring levels of stress in the wild.

Susceptibility of the male fitness phenotype to spontaneous mutation

Adult reproductive success can account for a large fraction of male fitness, however, we know relatively little about the susceptibility of reproductive traits to mutation-accumulation (MA). Estimates of the mutational rate of decline for adult fitness and its components are controversial in Drosophila melanogaster, and post-copulatory performance has not been examined. We therefore separately measured the consequences of MA for total male reproductive success and its major pre-copulatory and post-copulatory components: mating success and sperm competitive success. We also measured juvenile viability, an important fitness component that has been well studied in MA experiments. MA had strongly deleterious effects on both male viability and adult fitness, but the latter declined at a much greater rate. Mutational pressure on total fitness is thus much greater than would be predicted by viability alone. We also noted a significant and positive correlation between all adult traits and viability in the MA lines, suggesting pleiotropy of mutational effect as required by 'good genes' models of sexual selection.

Experimental mutation-accumulation on the X chromosome of Drosophila melanogaster reveals stronger selection on males than females

Background

Sex differences in the magnitude or direction of mutational effect may be important to a variety of population processes, shaping the mutation load and affecting the cost of sex itself. These differences are expected to be greatest after sexual maturity. Mutation-accumulation (MA) experiments provide the most direct way to examine the consequences of new mutations, but most studies have focused on juvenile viability without regard to sex, and on autosomes rather than sex chromosomes; both adult fitness and X-linkage have been little studied. We therefore investigated the effects of 50 generations of X-chromosome mutation accumulation on the fitness of males and females derived from an outbred population of Drosophila melanogaster.

Results

Fitness declined rapidly in both sexes as a result of MA, but adult males showed markedly greater fitness loss relative to their controls compared to females expressing identical genotypes, even when females were made homozygous for the X. We estimate that these mutations are partially additive (h ~ 0.3) in females. In addition, the majority of new mutations appear to harm both males and females.

Conclusions

Our data helps fill a gap in our understanding of the consequences of sexual selection for genetic load, and suggests that stronger selection on males may indeed purge deleterious mutations affecting female fitness.

Switch between life history strategies due to changes in glycolytic enzyme gene dosage in Saccharomyces cerevisiae

Adaptation is the process whereby a population or species becomes better fitted to its habitat through modifications of various life history traits which can be positively or negatively correlated. The molecular factors underlying these covariations remain to be elucidated. Using Saccharomyces cerevisiae as a model system, we have investigated the effects on life history traits of varying the dosage of genes involved in the transformation of resources into energy. Changing gene dosage for each of three glycolytic enzyme genes (hexokinase 2, phosphoglucose isomerase, and fructose-1,6-bisphosphate aldolase) resulted in variation in enzyme activities, glucose consumption rate, and life history traits (growth rate, carrying capacity, and cell size). However, the range of effects depended on which enzyme was expressed differently. Most interestingly, these changes revealed a genetic trade-off between carrying capacity and cell size, supporting the discovery of two extreme life history strategies already described in yeast populations: the "ants," which have lower glycolytic gene dosage, take up glucose slowly, and have a small cell size but reach a high carrying capacity, and the "grasshoppers," which have higher glycolytic gene dosage, consume glucose more rapidly, and allocate it to a larger cell size but reach a lower carrying capacity. These results demonstrate antagonist pleiotropy for glycolytic genes and show that altered dosage of a single gene drives a switch between two life history strategies in yeast.

Regeneration of the variance of metric traits by spontaneous mutation in a Drosophila population

In the C1 population of Drosophila melanogaster of moderate effective size (≈500), which was genetically invariant in its origin, we studied the regeneration by spontaneous mutation of the genetic variance for two metric traits [abdominal (AB) and sternopleural (ST) bristle number] and that of the concealed mutation load for viability, together with their temporal stability, using alternative selection models based on mutational parameters estimated in the C1 genetic background. During generations 381–485 of mutation accumulation (MA), the additive variances of AB and ST approached the levels observed in standing laboratory populations, fluctuating around their expected equilibrium values under neutrality or under relatively weak causal stabilizing selection. This type of selection was required to simultaneously account for the observed additive variance in our population and for those previously reported in natural and laboratory populations, indicating that most mutations affecting bristle traits would only be subjected to weak selective constraints. Although gene action for bristles was essentially additive, transient situations occurred where inbreeding resulted in a depression of the mean and an increase of the additive variance. This was ascribed to the occasional segregation of mutations of large recessive effects. On the other hand, the observed non-lethal inbreeding depression for viability must be explained by the segregation of alleles of considerable and largely recessive deleterious effects, and the corresponding load concealed in the heterozygous condition was found to be temporally stable, as expected from tighter constraints imposed by natural selection.

Measurements of spontaneous rates of mutations in the recent past and the near future

The rate of spontaneous mutation in natural populations is a fundamental parameter for many evolutionary phenomena. Because the rate of mutation is generally low, most of what is currently known about mutation has been obtained through indirect, complex and imprecise methodological approaches. However, in the past few years genome-wide sequencing of closely related individuals has made it possible to estimate the rates of mutation directly at the level of the DNA, avoiding most of the problems associated with using indirect methods. Here, we review the methods used in the past with an emphasis on next generation sequencing, which may soon make the accurate measurement of spontaneous mutation rates a matter of routine.

Rate and effects of spontaneous mutations that affect fitness in mutator Escherichia coli

Knowledge of the mutational parameters that affect the evolution of organisms is of key importance in understanding the evolution of several characteristics of many natural populations, including recombination and mutation rates. In this study, we estimated the rate and mean effect of spontaneous mutations that affect fitness in a mutator strain of Escherichia coli and review some of the estimation methods associated with mutation accumulation (MA) experiments. We performed an MA experiment where we followed the evolution of 50 independent mutator lines that were subjected to repeated bottlenecks of a single individual for approximately 1150 generations. From the decline in mean fitness and the increase in variance between lines, we estimated a minimum mutation rate to deleterious mutations of 0.005 (+/-0.001 with 95% confidence) and a maximum mean fitness effect per deleterious mutation of 0.03 (+/-0.01 with 95% confidence). We also show that any beneficial mutations that occur during the MA experiment have a small effect on the estimate of the rate and effect of deleterious mutations, unless their rate is extremely large. Extrapolating our results to the wild-type mutation rate, we find that our estimate of the mutational effects is slightly larger and the inferred deleterious mutation rate slightly lower than previous estimates obtained for non-mutator E. coli.

Distribution of fitness effects caused by single-nucleotide substitutions in bacteriophage f1

Empirical knowledge of the fitness effects of mutations is important for understanding many evolutionary processes, yet this knowledge is often hampered by several sources of measurement error and bias. Most of these problems can be solved using site-directed mutagenesis to engineer single mutations, an approach particularly suited for viruses due to their small genomes. Here, we used this technique to measure the fitness effect of 100 single-nucleotide substitutions in the bacteriophage f1, a filamentous single-strand DNA virus. We found that approximately one-fifth of all mutations are lethal. Viable ones reduced fitness by 11% on average and were accurately described by a log-normal distribution. More than 90% of synonymous substitutions were selectively neutral, while those affecting intergenic regions reduced fitness by 14% on average. Mutations leading to amino acid substitutions had an overall mean deleterious effect of 37%, which increased to 45% for those changing the amino acid polarity. Interestingly, mutations affecting early steps of the infection cycle tended to be more deleterious than those affecting late steps. Finally, we observed at least two beneficial mutations. Our results confirm that high mutational sensitivity is a general property of viruses with small genomes, including RNA and single-strand DNA viruses infecting animals, plants, and bacteria.

Polymorphic genes of major effect: consequences for variation, selection and evolution in Arabidopsis thaliana

The importance of genes of major effect for evolutionary trajectories within and among natural populations has long been the subject of intense debate. For example, if allelic variation at a major-effect locus fundamentally alters the structure of quantitative trait variation, then fixation of a single locus can have rapid and profound effects on the rate or direction of subsequent evolutionary change. Using an Arabidopsis thaliana RIL mapping population, we compare G-matrix structure between lines possessing different alleles at ERECTA, a locus known to affect ecologically relevant variation in plant architecture. We find that the allele present at ERECTA significantly alters G-matrix structure-in particular the genetic correlations between branch number and flowering time traits-and may also modulate the strength of natural selection on these traits. Despite these differences, however, when we extend our analysis to determine how evolution might differ depending on the ERECTA allele, we find that predicted responses to selection are similar. To compare responses to selection between allele classes, we developed a resampling strategy that incorporates uncertainty in estimates of selection that can also be used for statistical comparisons of G matrices.

Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines

We inferred the rate and properties of new spontaneous mutations in Drosophila melanogaster by carrying out whole-genome shotgun sequencing-by-synthesis of three mutation accumulation (MA) lines that had been maintained by close inbreeding for an average of 262 generations. We tested for the presence of new mutations by generating alignments of each MA line to the D. melanogaster reference genome sequence and then compared these alignments base by base. We determined empirically that at least five reads at a site within each line are required for accurate single nucleotide mutation calling. We mapped a total of 174 single-nucleotide mutations, giving a single nucleotide mutation rate of 3.5 x 10(-9) per site per generation. There were no false positives in a random sample of 40 of these mutations checked by Sanger sequencing. Variation in the numbers of mutations among the MA lines was small and nonsignificant. Numbers of transition and transversion mutations were 86 and 88, respectively, implying that transition mutation rate is close to 2x the transversion rate. We observed 1.5x as many G or C --> A or T as A or T --> G or C mutations, implying that the G or C --> A or T mutation rate is close to 2x the A or T --> G or C mutation rate. The base composition of the genome is therefore not at an equilibrium determined solely by mutation. The predicted G + C content at mutational equilibrium (33%) is similar to that observed in transposable element remnants. Nearest-neighbor mutational context dependencies are nonsignificant, suggesting that this is a weak phenomenon in Drosophila. We also saw nonsignificant differences in the mutation rate between transcribed and untranscribed regions, implying that any transcription-coupled repair process is weak. Of seven short indel mutations confirmed, six were deletions, consistent with the deletion bias that is thought to exist in Drosophila.

Direct estimation of the mitochondrial DNA mutation rate in Drosophila melanogaster

Mitochondrial DNA (mtDNA) variants are widely used in evolutionary genetics as markers for population history and to estimate divergence times among taxa. Inferences of species history are generally based on phylogenetic comparisons, which assume that molecular evolution is clock-like. Between-species comparisons have also been used to estimate the mutation rate, using sites that are thought to evolve neutrally. We directly estimated the mtDNA mutation rate by scanning the mitochondrial genome of Drosophila melanogaster lines that had undergone approximately 200 generations of spontaneous mutation accumulation (MA). We detected a total of 28 point mutations and eight insertion-deletion (indel) mutations, yielding an estimate for the single-nucleotide mutation rate of 6.2 × 10⁻⁸ per site per fly generation. Most mutations were heteroplasmic within a line, and their frequency distribution suggests that the effective number of mitochondrial genomes transmitted per female per generation is about 30. We observed repeated occurrences of some indel mutations, suggesting that indel mutational hotspots are common. Among the point mutations, there is a large excess of G→A mutations on the major strand (the sense strand for the majority of mitochondrial genes). These mutations tend to occur at nonsynonymous sites of protein-coding genes, and they are expected to be deleterious, so do not become fixed between species. The overall mtDNA mutation rate per base pair per fly generation in Drosophila is estimated to be about 10× higher than the nuclear mutation rate, but the mitochondrial major strand G→A mutation rate is about 70× higher than the nuclear rate. Silent sites are substantially more strongly biased towards A and T than nonsynonymous sites, consistent with the extreme mutation bias towards A+T. Strand-asymmetric mutation bias, coupled with selection to maintain specific nonsynonymous bases, therefore provides an explanation for the extreme base composition of the mitochondrial genome of Drosophila.

Mitochondria are the energy-producing organelles of the cell, and they contain genetic information encoded on their own genome. Because rates of mutation for mitochondrial genomes are believed to be much higher than those in nuclear DNA, mitochondrial genetic differences between and within species are particularly useful in population genetics, for example, as markers of population movements. We have directly estimated the mutation rate in the mitochondrial genome of the fruit fly Drosophila melanogaster in lines that had been allowed to randomly accumulate mutations in the virtual absence of effective natural selection. We scanned for new mutations by comparing the DNA of different lines by a sensitive mutation detection technique. We show that the mitochondrial mutation rate is about ten times higher than the nuclear DNA mutation rate. Strikingly, however, almost all of the single–base pair mutations that we detected change G to A at an amino acid site of a protein-coding gene. The explanation for this effect seems to be that natural selection maintains the nucleotide G at amino acid sites, whereas most silent sites are under weaker selection and have previously mutated to A or T. The mutation rate for G to A changes is 70 times higher than the nuclear DNA mutation rate. This extreme mutation bias maintains the high A+T content of the Drosophila mitochondrial genome.

We show that the mitochondrial DNA mutation rate in D. melanogaster is 10X higher than the nuclear mutation rate, and that major-strand G-->A hypermutablity explains the extremely biased base composition of the mitochondrial genome.

Analysis and implications of mutational variation

Variation from new mutations is important for several questions in quantitative genetics. Key parameters are the genomic mutation rate and the distribution of effects of mutations (DEM), which determine the amount of new quantitative variation that arises per generation from mutation (V(M)). Here, we review methods and empirical results concerning mutation accumulation (MA) experiments that have shed light on properties of mutations affecting quantitative traits. Surprisingly, most data on fitness traits from laboratory assays of MA lines indicate that the DEM is platykurtic in form (i.e., substantially less leptokurtic than an exponential distribution), and imply that most variation is produced by mutations of moderate to large effect. This finding contrasts with results from MA or mutagenesis experiments in which mutational changes to the DNA can be assayed directly, which imply that the vast majority of mutations have very small phenotypic effects, and that the distribution has a leptokurtic form. We compare these findings with recent approaches that attempt to infer the DEM for fitness based on comparing the frequency spectra of segregating nucleotide polymorphisms at putatively neutral and selected sites in population samples. When applied to data for humans and Drosophila, these analyses also indicate that the DEM is strongly leptokurtic. However, by combining the resultant estimates of parameters of the DEM with estimates of the mutation rate per nucleotide, the predicted V(M) for fitness is only a tiny fraction of V(M) observed in MA experiments. This discrepancy can be explained if we postulate that a few deleterious mutations of large effect contribute most of the mutational variation observed in MA experiments and that such mutations segregate at very low frequencies in natural populations, and effectively are never seen in population samples.

Phenotypic plasticity and genotype by environment interaction for olfactory behavior in Drosophila melanogaster

Genotype by environment interactions (GEI) play a major part in shaping the genetic architecture of quantitative traits and are confounding factors in genetic studies, for example, in attempts to associate genetic variation with disease susceptibility. It is generally not known what proportion of phenotypic variation is due to GEI and how many and which genes contribute to GEI. Behaviors are complex traits that mediate interactions with the environment and, thus, are ideally suited for studies of GEI. Olfactory behavior in Drosophila melanogaster presents an opportunity to systematically dissect GEI, since large numbers of genetically identical individuals can be reared under defined environmental conditions and the olfactory system of Drosophila and its behavioral response to odorants have been well characterized. We assessed variation in olfactory behavior in a population of 41 wild-derived inbred lines and asked to what extent different larval-rearing environments would influence adult olfactory behavior and whether GEI is a minor or major contributing source of phenotypic variation. We found that approximately 50% of phenotypic variation in adult olfactory behavior is attributable to GEI. In contrast, transcriptional analysis revealed that only 20 genes show GEI at the level of gene expression [false discovery rate (FDR) < 0.05], some of which are associated with physiological responses to environmental chemicals. Quantitative complementation tests with piggyBac-tagged mutants for 2 of these genes (CG9664 and Transferrin 1) demonstrate that genes that show transcriptional GEI are candidate genes for olfactory behavior and that GEI at the level of gene expression is correlated with GEI at the level of phenotype.

The dynamics of the roo transposable element in mutation-accumulation lines and segregating populations of Drosophila melanogaster

We estimated the number of copies for the long terminal repeat (LTR) retrotransposable element roo in a set of long-standing Drosophila melanogaster mutation-accumulation full-sib lines and in two large laboratory populations maintained with effective population size approximately 500, all of them derived from the same isogenic origin. Estimates were based on real-time quantitative PCR and in situ hybridization. Considering previous estimates of roo copy numbers obtained at earlier stages of the experiment, the results imply a strong acceleration of the insertion rate in the accumulation lines. The detected acceleration is consistent with a model where only one (maybe a few) of the approximately 70 roo copies in the ancestral isogenic genome was active and each active copy caused new insertions with a relatively high rate ( approximately 10(-2)), with new inserts being active copies themselves. In the two laboratory populations, however, a stabilized copy number or no accelerated insertion was found. Our estimate of the average deleterious viability effects per accumulated insert [E(s) < 0.003] is too small to account for the latter finding, and we discuss the mechanisms that could contain copy number.

The mutation matrix and the evolution of evolvability

Evolvability is a key characteristic of any evolving system, and the concept of evolvability serves as a unifying theme in a wide range of disciplines related to evolutionary theory. The field of quantitative genetics provides a framework for the exploration of evolvability with the promise to produce insights of global importance. With respect to the quantitative genetics of biological systems, the parameters most relevant to evolvability are the G-matrix, which describes the standing additive genetic variances and covariances for a suite of traits, and the M-matrix, which describes the effects of new mutations on genetic variances and covariances. A population's immediate response to selection is governed by the G-matrix. However, evolvability is also concerned with the ability of mutational processes to produce adaptive variants, and consequently the M-matrix is a crucial quantitative genetic parameter. Here, we explore the evolution of evolvability by using analytical theory and simulation-based models to examine the evolution of the mutational correlation, r(mu), the key parameter determining the nature of genetic constraints imposed by M. The model uses a diploid, sexually reproducing population of finite size experiencing stabilizing selection on a two-trait phenotype. We assume that the mutational correlation is a third quantitative trait determined by multiple additive loci. An individual's value of the mutational correlation trait determines the correlation between pleiotropic effects of new alleles when they arise in that individual. Our results show that the mutational correlation, despite the fact that it is not involved directly in the specification of an individual's fitness, does evolve in response to selection on the bivariate phenotype. The mutational variance exhibits a weak tendency to evolve to produce alignment of the M-matrix with the adaptive landscape, but is prone to erratic fluctuations as a consequence of genetic drift. The interpretation of this result is that the evolvability of the population is capable of a response to selection, and whether this response results in an increase or decrease in evolvability depends on the way in which the bivariate phenotypic optimum is expected to move. Interestingly, both analytical and simulation results show that the mutational correlation experiences disruptive selection, with local fitness maxima at -1 and +1. Genetic drift counteracts the tendency for the mutational correlation to persist at these extreme values, however. Our results also show that an evolving M-matrix tends to increase stability of the G-matrix under most circumstances. Previous studies of G-matrix stability, which assume nonevolving M-matrices, consequently may overestimate the level of instability of G relative to what might be expected in natural systems. Overall, our results indicate that evolvability can evolve in natural systems in a way that tends to result in alignment of the G-matrix, the M-matrix, and the adaptive landscape, and that such evolution tends to stabilize the G-matrix over evolutionary time.

The build up of mutation-selection- drift balance in laboratory Drosophila populations

The build up of an equilibrium between mutation, selection, and drift in populations of moderate size is an important evolutionary issue, and can be critical in the conservation of endangered populations. We studied this process in two Drosophila melanogaster populations initially lacking genetic variability (C1 and C2) that were subsequently maintained during 431 or 165 generations with effective population size N(e) approximately 500 (estimated by lethal complementation analysis). Each population originated synchronously to a companion set of full-sib mutation accumulation (MA) lines, C1 and MA1 were derived from an isogenic origin and C2 and MA2 from a single MA1 line at generation 265. The results suggest that both C1 and C2 populations were close to the mutation-selection-drift balance for viability and bristle traits, and are consistent with a 2.5-fold increase of the mutation rate in C2 and MA2. Despite this increase, the average panmictic viability in C2 was only slightly below that of C1, indicating that the expressed loads due to segregating deleterious mutation were small, in agreement with the low deleterious mutation rate (0.015-0.045) previously reported for the MA1 lines. In C1, the nonlethal inbreeding depression rate for viability was 30% of that usually estimated in segregating populations. The genetic variance for bristles regenerated in C1 and C2 was moderately smaller than the average value reported for natural populations, implying that they have accumulated a substantial adaptive potential. In light of neutral and selective predictions, these results suggest that bristle additive variance was predominantly due to segregation of mutations with deleterious effects of the order of 10(-3), and is consistent with relatively weak causal stabilizing selection (V(s) approximately 30).

Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila

Spontaneous mutations are the source of genetic variation required for evolutionary change, and are therefore important for many aspects of evolutionary biology. For example, the divergence between taxa at neutrally evolving sites in the genome is proportional to the per nucleotide mutation rate, u (ref. 1), and this can be used to date speciation events by assuming a molecular clock. The overall rate of occurrence of deleterious mutations in the genome each generation (U) appears in theories of nucleotide divergence and polymorphism, the evolution of sex and recombination, and the evolutionary consequences of inbreeding. However, estimates of U based on changes in allozymes or DNA sequences and fitness traits are discordant. Here we directly estimate u in Drosophila melanogaster by scanning 20 million bases of DNA from three sets of mutation accumulation lines by using denaturing high-performance liquid chromatography. From 37 mutation events that we detected, we obtained a mean estimate for u of 8.4 x 10(-9) per generation. Moreover, we detected significant heterogeneity in u among the three mutation-accumulation-line genotypes. By multiplying u by an estimate of the fraction of mutations that are deleterious in natural populations of Drosophila, we estimate that U is 1.2 per diploid genome. This high rate suggests that selection against deleterious mutations may have a key role in explaining patterns of genetic variation in the genome, and help to maintain recombination and sexual reproduction.

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 effect of antagonistic pleiotropy on the estimation of the average coefficient of dominance of deleterious mutations

We investigate the impact of antagonistic pleiotropy on the most widely used methods of estimation of the average coefficient of dominance of deleterious mutations from segregating populations. A proportion of the deleterious mutations affecting a given studied fitness component are assumed to have an advantageous effect on another one, generating overdominance on global fitness. Using diffusion approximations and transition matrix methods, we obtain the distribution of gene frequencies for nonpleiotropic and pleiotropic mutations in populations at the mutation-selection-drift balance. From these distributions we build homozygous and heterozygous chromosomes and assess the behavior of the estimators of dominance. A very small number of deleterious mutations with antagonistic pleiotropy produces substantial increases on the estimate of the average degree of dominance of mutations affecting the fitness component under study. For example, estimates are increased three- to fivefold when 2% of segregating loci are over-dominant for fitness. In contrast, strengthening pleiotropy, where pleiotropic effects are assumed to be also deleterious, has little effect on the estimates of the average degree of dominance, supporting previous results. The antagonistic pleiotropy model considered, applied under mutational parameters described in the literature, produces patterns for the distribution of chromosomal viabilities, levels of genetic variance, and homozygous mutation load generally consistent with those observed empirically for viability in Drosophila melanogaster.

Epistatic interactions among herbicide resistances in Arabidopsis thaliana: the fitness cost of multiresistance

The type of interactions among deleterious mutations is considered to be crucial in numerous areas of evolutionary biology, including the evolution of sex and recombination, the evolution of ploidy, the evolution of selfing, and the conservation of small populations. Because the herbicide resistance genes could be viewed as slightly deleterious mutations in the absence of the pesticide selection pressure, the epistatic interactions among three herbicide resistance genes (acetolactate synthase CSR, cellulose synthase IXR1, and auxin-induced AXR1 target genes) were estimated in both the homozygous and the heterozygous states, giving 27 genotype combinations in the model plant Arabidopsis thaliana. By analyzing eight quantitative traits in a segregating population for the three herbicide resistances in the absence of herbicide, we found that most interactions in both the homozygous and the heterozygous states were best explained by multiplicative effects (each additional resistance gene causes a comparable reduction in fitness) rather than by synergistic effects (each additional resistance gene causes a disproportionate fitness reduction). Dominance coefficients of the herbicide resistance cost ranged from partial dominance to underdominance, with a mean dominance coefficient of 0.07. It was suggested that the csr1-1, ixr1-2, and axr1-3 resistance alleles are nearly fully recessive for the fitness cost. More interestingly, the dominance of a specific resistance gene in the absence of herbicide varied according to, first, the presence of the other resistance genes and, second, the quantitative trait analyzed. These results and their implications for multiresistance evolution are discussed in relation to the maintenance of polymorphism at resistance loci in a heterogeneous environment.

A measure of the within-chromosome synergistic epistasis for Drosophila viability

In order to detect possible synergistic epistasis for viability in Drosophila melanogaster we assayed the relative viability of chromosomes II in: (i) panmixia, (ii) forced total homozygosity, and (iii) homozygosity for, on the average, half of their loci. As these genotypes were constructed using exactly the same set of chromosomes in the three cases, the design allows us to estimate the inbreeding depression rate at two different inbreeding levels in the absence of purging natural selection. Overall, no consistent synergistic epistasis was found. However, there was a small fraction of chromosomes whose severely deleterious effect when homozygous was almost significantly larger than expected from their viability when homozygous for half of their loci. This suggests occasional but important synergistic epistasis, which might confer evolutionary advantage to recombination in tightly linked genomes. Nevertheless, such epistasis is unlikely to be an evolutionary advantage driving the evolution of sexual anisogamous reproduction, as its contribution to overall viability is small when compared with the two-fold cost of anisogamy.

Spontaneous mutational correlations for life-history, morphological and behavioral characters in Caenorhabditis elegans

The pattern of mutational covariance among traits plays a central, but largely untested, role in many theories in evolutionary genetics. Here we estimate the pattern of phenotypic, environmental, and mutational correlations for a set of life-history, behavioral, and morphological traits using 67 self-fertilizing lines of Caenorhabditis elegans, each having independently experienced an average of 370 generations of spontaneous mutation accumulation. Bivariate relationships of mutational effects indicate the existence of extensive pleiotropy. We find that mutations may tend to produce manifold effects on suites of functionally related traits; however, our data do not support the idea of completely parcelated pleiotropy, in which functional units are separately affected by mutations. Positive net phenotypic and mutational correlations are common for life-history traits, with environmental correlations being comparatively smaller and of the same sign for most pairs of traits. Observed mutational correlations are shown to be higher than those produced by the chance accumulation of nonpleiotropic mutations in the same lines.

Analysis of the estimators of the average coefficient of dominance of deleterious mutations

We investigate the sources of bias that affect the most commonly used methods of estimation of the average degree of dominance (h) of deleterious mutations, focusing on estimates from segregating populations. The main emphasis is on the effect of the finite size of the populations, but other sources of bias are also considered. Using diffusion approximations to the distribution of gene frequencies in finite populations as well as stochastic simulations, we assess the behavior of the estimators obtained from populations at mutation-selection-drift balance under different mutational scenarios and compare averages of h for newly arisen and segregating mutations. Because of genetic drift, the inferences concerning newly arisen mutations based on the mutation-selection balance theory can have substantial upward bias depending upon the distribution of h. In addition, estimates usually refer to h weighted by the homozygous deleterious effect in different ways, so that inferences are complicated when these two variables are negatively correlated. Due to both sources of bias, the widely used regression of heterozygous on homozygous means underestimates the arithmetic mean of h for segregating mutations, in contrast to their repeatedly assumed equality in the literature. We conclude that none of the estimators from segregating populations provides, under general conditions, a useful tool to ascertain the properties of the degree of dominance, either for segregating or for newly arisen deleterious mutations. Direct estimates of the average h from mutation-accumulation experiments are shown to suffer some bias caused by purging selection but, because they do not require assumptions on the causes maintaining segregating variation, they appear to give a more reliable average dominance for newly arisen mutations.

The speed of adaptation in large asexual populations

In large asexual populations, beneficial mutations have to compete with each other for fixation. Here, I derive explicit analytic expressions for the rate of substitution and the mean beneficial effect of fixed mutations, under the assumptions that the population size N is large, that the mean effect of new beneficial mutations is smaller than the mean effect of new deleterious mutations, and that new beneficial mutations are exponentially distributed. As N increases, the rate of substitution approaches a constant, which is equal to the mean effect of new beneficial mutations. The mean effect of fixed mutations continues to grow logarithmically with N. The speed of adaptation, measured as the change of log fitness over time, also grows logarithmically with N for moderately large N, and it grows double-logarithmically for extremely large N. Moreover, I derive a simple formula that determines whether at given N beneficial mutations are expected to compete with each other or go to fixation independently. Finally, I verify all results with numerical simulations.

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.

Experimental studies of deleterious mutation in Saccharomyces cerevisiae

Yeast has proven to be a very useful model organism for studying eukaryotic cell functions. Its applicability for population and quantitative genetics is less well known. Among its advantages is the ease of screening for mutants. The present paper reviews experiments aimed at estimating the parameters of spontaneous mutations deleterious to fitness. The rate of deleterious mutation was found to be moderately high. A large fraction of detectable mutants were lethal; among the non-lethal mutants, the least harmful ones dominated. Deleterious mutations, and especially the lethal ones, were generally very well masked by wild-type alleles when in heterozygous loci. The negative effects of mutations were much stronger under stressful than under benign conditions. Interactions between loci with deleterious mutations did alter their fitness, but no strong overall effect of synergism or antagonisms was observed.

The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus

Little is known about the mutational fitness effects associated with single-nucleotide substitutions on RNA viral genomes. Here, we used site-directed mutagenesis to create 91 single mutant clones of vesicular stomatitis virus derived from a common ancestral cDNA and performed competition experiments to measure the relative fitness of each mutant. The distribution of nonlethal deleterious effects was highly skewed and had a long, flat tail. As expected, fitness effects depended on whether mutations were chosen at random or reproduced previously described ones. The effect of random deleterious mutations was well described by a log-normal distribution, with -19% reduction of average fitness; the effects distribution of preobserved deleterious mutations was better explained by a beta model. The fit of both models was improved when combined with a uniform distribution. Up to 40% of random mutations were lethal. The proportion of beneficial mutations was unexpectedly high. Beneficial effects followed a gamma distribution, with expected fitness increases of 1% for random mutations and 5% for preobserved mutations.

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.

FITNESS AND ADAPTATION IN A NOVEL ENVIRONMENT: EFFECT OF INBREEDING, PRIOR ENVIRONMENT, AND LINEAGE

The ability of populations to undergo adaptive evolution depends on the presence of genetic variation for ecologically important traits. The maintenance of genetic variation may be influenced by many variables, particularly long-term effective population size and the strength and form of selection. The roles of these factors are controversial and there is very little information on their impacts for quantitative characters. The aims of this study were to determine the impacts of population size and variable versus constant prior environmental conditions on fitness and the magnitude of response to selection. Outbred and inbred populations of Drosophila melanogaster were maintained under benign, constant stressful, and variably stressful conditions for seven generations, and then forced to adapt to a novel stress for seven generations. Fitness and adaptability were assayed in each replicate population. Our findings are that: (1) populations inbred in a variable environment were more adaptable than those inbred in a constant environment; (2) populations adapted to a prior stressful environment had greater fitness when reared in a novel stress than those less adapted to stress; (3) inbred populations had lower fitness and were less adaptable than the outbred population they were derived from; and (4) strong lineage effects were detectable across environments in the inbred populations.

Comparing analysis methods for mutation-accumulation data: a simulation study

We simulated single-generation data for a fitness trait in mutation-accumulation (MA) experiments, and we compared three methods of analysis. Bateman-Mukai (BM) and maximum likelihood (ML) need information on both the MA lines and control lines, while minimum distance (MD) can be applied with or without the control. Both MD and ML assume gamma-distributed mutational effects. ML estimates of the rate of deleterious mutation had larger mean square error (MSE) than MD or BM had due to large outliers. MD estimates obtained by ignoring the mean decline observed from comparison to a control are often better than those obtained using that information. When effects are simulated using the gamma distribution, reducing the precision with which the trait is assayed increases the probability of obtaining no ML or MD estimates but causes no appreciable increase of the MSE. When the residual errors for the means of the simulated lines are sampled from the empirical distribution in a MA experiment, instead of from a normal one, the MSEs of BM, ML, and MD are practically unaffected. When the simulated gamma distribution accounts for a high rate of mild deleterious mutation, BM detects only approximately 30% of the true deleterious mutation rate, while MD or ML detects substantially larger fractions. To test the robustness of the methods, we also added a high rate of common contaminant mutations with constant mild deleterious effect to a low rate of mutations with gamma-distributed deleterious effects and moderate average. In that case, BM detects roughly the same fraction as before, regardless of the precision of the assay, while ML fails to provide estimates. However, MD estimates are obtained by ignoring the control information, detecting approximately 70% of the total mutation rate when the mean of the lines is assayed with good precision, but only 15% for low-precision assays. Contaminant mutations with only tiny deleterious effects could not be detected with acceptable accuracy by any of the above methods.

Rapid fitness recovery in mutationally degraded lines of Caenorhabditis elegans

Deleterious mutation accumulation has been implicated in many biological phenomena and as a potentially significant threat to human health and the persistence of small populations. The vast majority of mutations with effects on fitness are known to be deleterious in a given environment, and their accumulation results in mean population fitness decline. However, whether populations are capable of recovering from negative effects of prolonged genetic bottlenecks via beneficial or compensatory mutation accumulation has not previously been tested. To address this question, long-term mutation-accumulation lines of the nematode Caenorhabditis elegans, previously propagated as single individuals each generation, were maintained in large population sizes under competitive conditions. Fitness assays of these lines and comparison to parallel mutation-accumulation lines and the ancestral control show that, while the process of fitness restoration was incomplete for some lines, full recovery of mean fitness was achieved in fewer than 80 generations. Several lines of evidence indicate that this fitness restoration was at least partially driven by compensatory mutation accumulation rather than a result of a generic form of laboratory adaptation. This surprising result has broad implications for the influence of the mutational process on many issues in evolutionary and conservation biology.

Lack of nonadditive genetic effects on early fecundity in Drosophila melanogaster

Fecundity is usually considered as a trait closely connected to fitness and is expected to exhibit substantial nonadditive genetic variation and inbreeding depression. However, two independent experiments, using populations of different geographical origin, indicate that early fecundity in Drosophila melanogaster behaves as a typical additive trait of low heritability. The first experiment involved artificial selection in inbred and non-inbred lines, all of them started from a common base population previously maintained in the laboratory for about 35 generations. The realized heritability estimate was 0.151 +/- 0.075 and the inbreeding depression was very small and nonsignificant (0.09 +/- 0.09% of the non-inbred mean per 1% increase in inbreeding coefficient). With inbreeding, the observed decrease in the within-line additive genetic variance and the corresponding increase of the between-line variance were very close to their expected values for pure additive gene action. This result is at odds with previous studies showing inbreeding depression and, therefore, directional dominance for the same trait and species. All experiments, however, used laboratory populations, and it is possible that the original genetic architecture of the trait in nature was subsequently altered by the joint action of random drift and adaptation to captivity. Thus, we carried out a second experiment, involving inbreeding without artificial selection in a population recently collected from the wild. In this case we obtained, again, a maximum-likelihood heritability estimate of 0.210 +/- 0.027 and very little nonsignificant inbreeding depression (0.06 +/- 0.12%). The results suggest that, for fitness-component traits, low levels of additive genetic variance are not necessarily associated with large inbreeding depression or high levels of nonadditive genetic variance.