The genetic structure of natural populations of Drosophila melanogaster. 8. Natural selection on the degree of dominance of viability polygenes

The variability is in the sex chromosomes

Sex differences in the mean trait expression are well documented, not only for traits that are directly associated with reproduction. Less is known about how the variability of traits differs between males and females. In species with sex chromosomes and dosage compensation, the heterogametic sex is expected to show larger trait variability ("sex-chromosome hypothesis"), yet this central prediction, based on fundamental genetic principles, has never been evaluated in detail. Here we show that in species with heterogametic males, male variability in body size is significantly larger than in females, whereas the opposite can be shown for species with heterogametic females. These results support the prediction of the sex-chromosome hypothesis that individuals of the heterogametic sex should be more variable. We argue that the pattern demonstrated here for sex-specific body size variability is likely to apply to any trait and needs to be considered when testing predictions about sex-specific variability and sexual selection.

Sex-differential selection and the evolution of X inactivation strategies

X inactivation—the transcriptional silencing of one X chromosome copy per female somatic cell—is universal among therian mammals, yet the choice of which X to silence exhibits considerable variation among species. X inactivation strategies can range from strict paternally inherited X inactivation (PXI), which renders females haploid for all maternally inherited alleles, to unbiased random X inactivation (RXI), which equalizes expression of maternally and paternally inherited alleles in each female tissue. However, the underlying evolutionary processes that might account for this observed diversity of X inactivation strategies remain unclear. We present a theoretical population genetic analysis of X inactivation evolution and specifically consider how conditions of dominance, linkage, recombination, and sex-differential selection each influence evolutionary trajectories of X inactivation. The results indicate that a single, critical interaction between allelic dominance and sex-differential selection can select for a broad and continuous range of X inactivation strategies, including unequal rates of inactivation between maternally and paternally inherited X chromosomes. RXI is favored over complete PXI as long as alleles deleterious to female fitness are sufficiently recessive, and the criteria for RXI evolution is considerably more restrictive when fitness variation is sexually antagonistic (i.e., alleles deleterious to females are beneficial to males) relative to variation that is deleterious to both sexes. Evolutionary transitions from PXI to RXI also generally increase mean relative female fitness at the expense of decreased male fitness. These results provide a theoretical framework for predicting and interpreting the evolution of chromosome-wide expression of X-linked genes and lead to several useful predictions that could motivate future studies of allele-specific gene expression variation.

With the exception of its most primitive members, mammal species practice X inactivation, where one copy of each X chromosome pair is silenced in each cell of the female body. The particular copy of the X that is silenced nevertheless shows considerable variability among species, and the evolutionary causes for this variability remain unclear. Here, we show that X inactivation strategies are likely to evolve in response to the sex-differential fitness properties of X-linked genetic variation. Genetic variation with similar effects on male and female fitness will generally favor the evolution of random X inactivation, potentially including preferential inactivation of the maternally inherited X chromosome. Variation with opposing fitness effects in each sex (“sexually antagonistic” variation, which includes mutations that both decrease female fitness and enhance male fitness) selects for preferential or complete inactivation of the paternally inherited X. Paternally biased X inactivation patterns appear to be common in nature, which suggests that sexually antagonistic genetic variation might be an important factor underlying the evolution of X inactivation. The theory provides a conceptual framework for understanding the evolution of X inactivation strategies and generates several novel predictions that may soon be tested with modern genome sequencing technologies.

Variance component analysis for viability in an isolated population ofDrosophila melanogaster

Using the 602 second chromosome lines extracted from the Ishigakijima population ofDrosophila melanogasterin Japan, partial diallel cross experiments (Design II of Comstock & Robinson, 1952) were carried out, and the additive genetic variance and the dominance variance of viability were estimated. The estimated value of the additive genetic variance is 0·01754±0·00608, and the dominance variance 0·00151±0·00114, using a logarithmic scale. Since the value of the additive genetic variance is much larger than expected under mutation–selection balance although the dominance variance is compatible with it, we speculate that in the Ishigakijima population some type of balancing selection must be operating to maintain the genetic variability with respect to viability at a minority of loci. As candidates for such selection, overdominance, frequency-dependent selection, and diversifying selection are considered, and it is suggested that diversifying selection is the most probable candidate for increasing the additive genetic variance.

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.

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.

Mutation-selection balance accounting for genetic variation for viability inDrosophila melanogasteras deduced from an inbreeding and artificial selection experiment

We carried out an experiment of inbreeding and upward artificial selection for egg-to-adult viability in a recently captured population of Drosophila melanogaster, as well as computer simulations of the experimental design, in order to obtain information on the nature of genetic variation for this important fitness component. The inbreeding depression was linear with a rate of 0.70 +/- 0.11% of the initial mean per 1% increase in inbreeding coefficient, and the realized heritability was 0.06 +/- 0.07. We compared the empirical observations of inbreeding depression and selection response with computer simulations assuming a balance between the occurrence of partially recessive deleterious mutations and their elimination by selection. Our results suggest that a model assuming mutation-selection balance with realistic mutational parameters can explain the genetic variation for viability in the natural population studied. Several mutational models are incompatible with some observations and can be discarded. Mutational models assuming a low rate of mutations of large average effect and highly recessive gene action, and others assuming a high rate of mutations of small average effect and close to additive gene action, are compatible with all the observations.

On the average coefficient of dominance of deleterious spontaneous mutations

T. Mukai and co-workers in the late 1960s and O. Ohnishi in the 1970s carried out a series of experiments to obtain direct estimates of the average coefficient of dominance (h) of minor viability mutations in Drosophila melanogaster. The results of these experiments, although inconsistent, have been interpreted as indicating slight recessivity of deleterious mutations, with h approximately 0.4. Mukai obtained conflicting results depending on the type of heterozygotes used, some estimates suggesting overdominance and others partial dominance. Ohnishi's estimates, based on the ratio of heterozygous to homozygous viability declines, were more consistent, pointing to the above value. However, we have reanalyzed Ohnishi's data, estimating h by the regression method, and obtained a much smaller estimate of approximately 0.1. This significant difference can be due partly to the different weighting implicit in the estimates, but we suggest that this is not the only explanation. We propose as a plausible hypothesis that a putative nonmutational decline in viability occurring in the first half of Ohnishi's experiment (affecting both homozygotes and heterozygotes) has biased upward the estimates from the ratio, while it would not bias the regression estimates. This hypothesis also explains the very high h approximately 0.7 observed in Ohnishi's high-viability chromosomes. By constructing a model of spontaneous mutations using parameters in the literature, we investigate the above possibility. The results indicate that a model of few mutations with moderately large effects and h approximately 0.2 is able to explain the observed estimates and the distributions of homozygous and heterozygous viabilities. Accounting for an expression of mutations in genotypes with the balancer chromosome Cy does not alter the conclusions qualitatively.

Bottleneck effect on genetic variance. A theoretical investigation of the role of dominance

The phenomenon that the genetic variance of fitness components increase following a bottleneck or inbreeding is supported by a growing number of experiments and is explained theoretically by either dominance or epistasis. In this article, diffusion approximations under the infinite sites model are used to quantify the effect of dominance, using data on viability in Drosophila melanogaster. The model is based on mutation parameters from mutation accumulation experiments involving balancer chromosomes (set I) or inbred lines (set II). In essence, set I assumes many mutations of small effect, whereas set II assumes fewer mutations of large effect. Compared to empirical estimates from large outbred populations, set I predicts reasonable genetic variances but too low mean viability. In contrast, set II predicts a reasonable mean viability but a low genetic variance. Both sets of parameters predict the changes in mean viability (depression), additive variance, between-line variance and heritability following bottlenecks generally compatible with empirical results, and these changes are mainly caused by lethals and deleterious mutants of large effect. This article suggests that dominance is the main cause for increased genetic variances for fitness components and fitness-related traits after bottlenecks observed in various experiments.

Genetic polymorphism and high detrimental load in natural populations of Drosophila melanogaster from cellar and vineyard

Two Spanish natural populations of Drosophila melanogaster have been analysed with respect to genetic variability in third chromosome viability. The two populations, although from the same locality, belong to relatively different habitats: the inside of a cellar and a vineyard. The patterns of homozygote and heterozygote viability are similar in both populations. The homozygous detrimental loads estimated are very high and the values for the D:L (detrimental/lethal) ratio close to 2.5, which is higher than any previously found. The environmental variance of viability, average degrees of dominance of lethal genes and of viability polygenes and effective population sizes were estimated in each population. The mechanisms which could maintain variability in these populations, the causes of the high detrimental loads and the possibility that cellar and vineyard could be two subpopulations of a larger population are discussed.

Rapid change in mutation rate in a local population of Drosophila melanogaster

The lethal and detrimental loads per second chromosome rapidly increased from 1968 to 1970 in a local population of Drosophila melanogaster in Japan (lethal load, from about 0.16 to 0.38; detrimental load, from 0.125 to 0.231 [Watanabe, T. K., Watanabe, T. & Oshima, C. (1976) Evolution 30, 109-118]). When the homozygous loads were measured in 1983, the lethal load had decreased to approximately the original amount (0.19) but the detrimental load had stayed high (0.241). The rise and fall of the lethal load can be accounted for by a P-type element that invaded a population with M cytotype, producing a high mutation rate. The mutation rate fell back to the earlier value after the cytotype became P. That the detrimental load did not decrease can be explained by assuming a longer persistence for detrimental mutations in the population. Evidence for a P-type mutator factor is that the mutation rate of the wild-type chromosomes differs between the different cytoplasmic and chromosomal backgrounds, being lower in the background from which the chromosomes were taken.

Spontaneous mutations modifying the activity of alcohol dehydrogenase (ADH) in Drosophila melanogaster

In a marked-inversion balanced lethal system of the second chromosome of Drosophila melanogaster, mutations were accumulated under minimum pressure of natural selection in 1000 individual lines that originated essentially from two individuals. After about 300 generations, the specific activities of alcohol dehydrogenase of 69 randomly selected individual lines were measured with replications using four replicated vials (on 2 days--two replications per day) by observing the reduction of NAD+ to NADH at 340 nm. Total soluble protein as the basis of standardization of enzyme activity was measured by the Lowry method for each vial. A control experiment was made immediately after the establishment of 20 individual lines from a single genotype. A significant increase in genetic variance was observed among the mutation-accumulating lines but was not detected in the control experiment. The statistical analysis of the data on the basis of the one-band/one-gene hypothesis suggests that many mutations controlling the activity of alcohol dehydrogenase occurred in regions different from the alcohol dehydrogenase locus itself, mainly in the noncoding DNA. Furthermore, it is suggested that transposon-like elements are related to the induction of these changes in alcohol dehydrogenase specific activities. Additional experimental evidence supporting this conclusion is also given.