Mutations Of Small Effect Research Articles

Accumulation of deleterious mutations: additional Drosophila melanogaster estimates and a simulation of the effects of selection.

We report an assay of egg-to-adult viability in full-sibling mutation accumulation (MA) lines derived from a completely homozygous population of Drosophila melanogaster and maintained for 210 generations. A simultaneous evaluation was also made of a large population derived from the same origin and maintained as a control for the same period. We also present computer simulations to explore the possible decline in viability of the control population due to mutation accumulation and the possible effect of selection within and between MA lines. For this purpose, we used two mutational models independent from the data analyzed and based on radically different assumptions. The first model implies a large number of mutations of small effect, whereas the second implies a much smaller number of mutations with much larger effects. The observed rate of decline in mean viability was very small but significant (0.077%). The rate of increase in among line variance (0.189 x 10(-3)) was similar to those obtained previously in the same lines. The simulation results indicated that a model of many mutations of small effect is incompatible with the evolution of the mean viability of the control and MA lines over generations, the distribution of line means after 210 generations of mutation accumulation, and the pattern of line extinction over generations. Basically, this model predicted a large drop in viability, both in the control and particularly the MA lines, that is not observed empirically. It also predicted a rate of line extinction too low in the early generations and too high in the later ones. In contrast, the model based on few mutations of large effect was generally consistent with all the observations.

Long-term Buildup of Reproductive Isolation Promoted by Disruptive Selection: How Far Does it Go?

We analyze the long-term evolution of a continuous trait subject to frequency-dependent disruptive selection, and controlled by a single diploid, additive locus. Our simple selection model is a mathematical approximation to many complex systems of ecological interactions resulting in disruptive selection, like, for example, scramble competition and habitat heterogeneity. A polymorphism of two specific alleles at equal frequencies is the unique long-term equilibrium, or ESS, of this system. We then study the evolution of direct assortative mating for the selected trait, through mutations of small effect at modifier loci controlling the degree of assortment. The mating process is described by a model that allows for possible costs of assortment. Unless the cost of assortment is too high, strength of assortment always increases in populations where mating is random or weakly assortative, and also in populations that already practice very strong assortative mating. However, even if it has no cost, assortment can increase continuously from random mating to complete isolation, resulting in sympatric speciation, only if selection is sufficiently strong. In fact, only a modest degree of assortment, corresponding to a continuously stable ESS, can be attained from random mating, when selection intensity is below a certain threshold.

ACCUMULATION OF DELETERIOUS MUTATIONS: ADDITIONAL DROSOPHILA MELANOGASTER ESTIMATES AND A SIMULATION OF THE EFFECTS OF SELECTION

We report an assay of egg-to-adult viability in full-sibling mutation accumulation (MA) lines derived from a completely homozygous population of Drosophila melanogaster and maintained for 210 generations. A simultaneous evaluation was also made of a large population derived from the same origin and maintained as a control for the same period. We also present computer simulations to explore the possible decline in viability of the control population due to mutation accumulation and the possible effect of selection within and between MA lines. For this purpose, we used two mutational models independent from the data analyzed and based on radically different assumptions. The first model implies a large number of mutations of small effect, whereas the second implies a much smaller number of mutations with much larger effects. The observed rate of decline in mean viability was very small but significant (0.077%). The rate of increase in among line variance (0.189 × 10−3) was similar to those obtained previously in the same lines. The simulation results indicated that a model of many mutations of small effect is incompatible with the evolution of the mean viability of the control and MA lines over generations, the distribution of line means after 210 generations of mutation accumulation, and the pattern of line extinction over generations. Basically, this model predicted a large drop in viability, both in the control and particularly the MA lines, that is not observed empirically. It also predicted a rate of line extinction too low in the early generations and too high in the later ones. In contrast, the model based on few mutations of large effect was generally consistent with all the observations.

THE POPULATION GENETICS OF ADAPTATION: THE ADAPTATION OF DNA SEQUENCES

I describe several patterns characterizing the genetics of adaptation at the DNA level. Following Gillespie (1983, 1984, 1991), I consider a population presently fixed for the ith best allele at a locus and study the sequential substitution of favorable mutations that results in fixation of the fittest DNA sequence locally available. Given a wild type sequence that is less than optimal, I derive the fitness rank of the next allele typically fixed by natural selection as well as the mean and variance of the jump in fitness that results when natural selection drives a substitution. Looking over the whole series of substitutions required to reach the best allele, I show that the mean fitness jumps occurring throughout an adaptive walk are constrained to a twofold window of values, assuming only that adaptation begins from a reasonably fit allele. I also show that the first substitution and the substitution of largest effect account for a large share of the total fitness increase during adaptation. I further show that the distribution of selection coefficients fixed throughout such an adaptive walk is exponential (ignoring mutations of small effect), a finding reminiscent of that seen in Fisher's geometric model of adaptation. Last, I show that adaptation by natural selection behaves in several respects as the average of two idealized forms of adaptation, perfect and random.

Clines in polygenic traits.

This article outlines theoretical models of clines in additive polygenic traits, which are maintained by stabilizing selection towards a spatially varying optimum. Clines in the trait mean can be accurately predicted, given knowledge of the genetic variance. However, predicting the variance is difficult, because it depends on genetic details. Changes in genetic variance arise from changes in allele frequency, and in linkage disequilibria. Allele frequency changes dominate when selection is weak relative to recombination, and when there are a moderate number of loci. With a continuum of alleles, gene flow inflates the genetic variance in the same way as a source of mutations of small effect. The variance can be approximated by assuming a Gaussian distribution of allelic effects; with a sufficiently steep cline, this is accurate even when mutation and selection alone are better described by the 'House of Cards' approximation. With just two alleles at each locus, the phenotype changes in a similar way: the mean remains close to the optimum, while the variance changes more slowly, and over a wider region. However, there may be substantial cryptic divergence at the underlying loci. With strong selection and many loci, linkage disequilibria are the main cause of changes in genetic variance. Even for strong selection, the infinitesimal model can be closely approximated by assuming a Gaussian distribution of breeding values. Linkage disequilibria can generate a substantial increase in genetic variance, which is concentrated at sharp gradients in trait means.

DNA polymorphism-diet-cofactor-development hypothesis and the gene-teratogen model for schizophrenia and other developmental disorders

Three problems in identifying genes causing schizophrenia and other developmental disorders may be locus heterogeneity, high disease allele frequency, and unknown mode of inheritance. The DNA polymorphism-diet-cofactor-development (DDCD) hypothesis addresses the first two. The gene-teratogen model addresses the third. The DDCD hypothesis is that schizophrenia results in part from brain abnormality in utero from the aggregate effect of multiple mutations of small effect of genes related to important cofactors (e.g., folate, cobalamin, or pyridoxine) potentiated by maternal dietary deficiency of these cofactors and by pregnancy. The effect results from insufficiency of the cofactors and from resulting effects such as impaired DNA synthesis, immune deficiency, effects on niacin and serotonin metabolism, and teratogens, e.g., hyperhomocysteinemia. The hypothesis addresses all of the unusual features of schizophrenia: e.g., decreased brain gray matter, birth-month effect, geographical differences, socioeconomic predilection, association with obstetrical abnormalities, decreased incidence of rheumatoid arthritis, and association with famine and viral epidemics. In the gene-teratogen model, a teratogenic effect in utero produces a developmental disorder through a teratogenic locus and a modifying or specificity locus, as well as through environmental factors. An example is the major intrauterine effect seen in offspring of phenylketonuric mothers. Thus, the mode of inheritance of genes acting prenatally may in some cases be fundamentally different from that of genes acting postnatally. The model is interesting because it is simple and because teratogenic loci will be difficult to locate by conventional linkage mapping techniques due to misspecification of the affection status of both mother and affected children. A new study design is suggested for identifying teratogenic loci.

DNA polymorphism‐diet‐cofactor‐development hypothesis and the gene‐teratogen model for schizophrenia and other developmental disorders

Three problems in identifying genes causing schizophrenia and other developmental disorders may be locus heterogeneity, high disease allele frequency, and unknown mode of inheritance. The DNA polymorphism-diet-cofactor-development (DDCD) hypothesis addresses the first two. The gene-teratogen model addresses the third. The DDCD hypothesis is that schizophrenia results in part from brain abnormality in utero from the aggregate effect of multiple mutations of small effect of genes related to important cofactors (e.g., folate, cobalamin, or pyridoxine) potentiated by maternal dietary deficiency of these cofactors and by pregnancy. The effect results from insufficiency of the cofactors and from resulting effects such as impaired DNA synthesis, immune deficiency, effects on niacin and serotonin metabolism, and teratogens, e.g., hyperhomocysteinemia. The hypothesis addresses all of the unusual features of schizophrenia: e.g., decreased brain gray matter, birth-month effect, geographical differences, socioeconomic predilection, association with obstetrical abnormalities, decreased incidence of rheumatoid arthritis, and association with famine and viral epidemics. In the gene-teratogen model, a teratogenic effect in utero produces a developmental disorder through a teratogenic locus and a modifying or specificity locus, as well as through environmental factors. An example is the major intrauterine effect seen in offspring of phenylketonuric mothers. Thus, the mode of inheritance of genes acting prenatally may in some cases be fundamentally different from that of genes acting postnatally. The model is interesting because it is simple and because teratogenic loci will be difficult to locate by conventional linkage mapping techniques due to misspecification of the affection status of both mother and affected children. A new study design is suggested for identifying teratogenic loci. Am. J. Med. Genet. (Neuropsychiatr. Genet.) 88:311–323, 1999. © 1999 Wiley-Liss, Inc.

Evolution by small steps and rugged landscapes in the RNA virus phi6.

Fisher's geometric model of adaptive evolution argues that adaptive evolution should generally result from the substitution of many mutations of small effect because advantageous mutations of small effect should be more common than those of large effect. However, evidence for both evolution by small steps and for Fisher's model has been mixed. Here we report supporting results from a new experimental test of the model. We subjected the bacteriophage phi6 to intensified genetic drift in small populations and caused viral fitness to decline through the accumulation of a deleterious mutation. We then propagated the mutated virus at a range of larger population sizes and allowed fitness to recover by natural selection. Although fitness declined in one large step, it was usually recovered in smaller steps. More importantly, step size during recovery was smaller with decreasing size of the recovery population. These results confirm Fisher's main prediction that advantageous mutations of small effect should be more common. We also show that the advantageous mutations of small effect are compensatory mutations whose advantage is conditional (epistatic) on the presence of the deleterious mutation, in which case the adaptive landscape of phi6 is likely to be very rugged.

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.

Mismatch repair and the accumulation of deleterious mutations influence the competitive advantage of MAT (mating type) heterozygosity in the yeast Saccharomyces cerevisiae.

Competitions between matched pairs of diploid strains of Saccharomyces cerevisiae, one capable of undergoing sexual recombination (MAT-heterozygous) and the other not (MAT-homozygous), have proved useful for measuring the effects of mitotic and meiotic recombination and DNA repair on competitive ability in this organism. Overall competitive differences between the strains can be enhanced by converting them to petites (aerobic respiration incompetent). Here we report the results of competitions between pairs of strains that also differ in their ability to undergo mismatch repair. In petite strains, the growth rates of mismatch-repair defective strains declined over time regardless of their MAT genotype. Mismatch-repair proficient MAT-heterozygous strains did not show a decline, while repair-deficient MAT-homozygous strains did. The decline appears to be due to the accumulation of deleterious mutations of small effect, which can be corrected by MAT-heterozygous strains having intact mismatch repair. The relative competitive abilities of MAT-heterozygous and MAT-homozygous strains diverged during the course of the competitions, and the variance of this divergence increased significantly when mismatch repair was defective. This large stochastic component indicates that a relatively small number of deleterious mutations may be involved. The accumulation of deleterious mutations and their subsequent repair may have a bearing on the origin of sex in this organism.

Inferences on genome-wide deleterious mutation rates in inbred populations of Drosophila and mice.

A theoretical analysis was carried out on the mutation load observed in long-maintained inbred lines from two experiments with Drosophila and mice. The rate of decline in fitness and its sampling distribution were predicted for both experiments using Monte Carlo simulation with a range of mutational parameters and models. The predicted rates of change in fitness were compared to the empirical observed rates, which were close to zero. The classical hypothesis of many deleterious mutations (about one event per genome per generation) of small effect (1-2%) resulting in a mutation pressure for fitness of about 1% per generation is incompatible with the data. Recent estimates suggesting an overall mutation pressure for fitness traits of about 0.1% are, however, compatible with the observed load.

Adaptive evolution via a major gene effect: paedomorphosis in the Mexican axolotl.

Although adaptive evolution is thought to depend primarily on mutations of small effect, major gene effects may underlie many of the important differences observed among species in nature. The Mexican axolotl (Ambystoma mexicanum) has a derived mode of development that is characterized by metamorphic failure (paedomorphosis), an adaptation for an entirely aquatic life cycle. By using an interspecific crossing design and genetic linkage analysis, a major quantitative trait locus for expression of metamorphosis was identified in a local map of amplified fragment length polymorphisms. These data are consistent with a major gene hypothesis for the evolution of paedomorphosis in A. mexicanum.

EVOLUTION OF GYNODIOECY AND MAINTENANCE OF FEMALES: THE ROLE OF INBREEDING DEPRESSION, OUTCROSSING RATES, AND RESOURCE ALLOCATION IN SCHIEDEA ADAMANTIS (CARYOPHYLLACEAE).

Levels of inbreeding depression, outcrossing rates, and phenotypic patterns of resource allocation were studied to examine their relative importance in the maintenance of high numbers of females in gynodioecious Schiedea adamantis (Caryophyllaceae), an endemic Hawaiian shrub found in a single population on Diamond Head Crater, Oahu. In studies of inbreeding depression in two greenhouse environments, families of hermaphrodites exhibited significant inbreeding depression (δ = 0.60), based on a multiplicative fitness function using seeds per capsule, germination, survival, and the inflorescence biomass of progeny. Differences between inbred and outcrossed progeny were smallest at the early stage of seeds per capsule and more pronounced at the later stages of survival and inflorescence production. These results are consistent with inbreeding depression caused by many mutations of small effect. Using allozyme analyses, the inbreeding coefficient of adult plants in the field was not significantly different from zero, implying that δ in nature may be equal to one. The single locus estimate of the outcrossing rate for hermaphrodites was 0.50 based on progeny that survived to flowering; corrected for the disproportionate loss before flowering of progeny from selfing, the adjusted outcrossing rate at the zygote stage was 0.32, suggesting that considerable selfing occurs in hermaphrodites. Females were totally outcrossed. When females and hermaphrodites were compared for reproductive output in the field, females produced over twice as many seeds per plant as hermaphrodites, primarily because females had far more capsules per inflorescence than hermaphrodites. Females had greater mass per seed than hermaphrodites in the field, either because of greater provisioning or reduced inbreeding depression. There was no significant differential mortality with respect to sex over a seven year period. The higher number of seeds per plant of females, combined with substantial inbreeding depression and relatively high selfing rates for hermaphrodites, are probably responsible for the maintenance of females in this population. The predicted frequency of females based on data for seed production, the adjusted selfing rate, and inbreeding depression is 42%, remarkably close to the observed frequency of 39%. High levels of inbreeding depression suggest that considerable quantitative genetic variation is present for traits affecting fitness in this population, despite low allozyme variability and a presumed founder effect.

Continuous Stability and Evolutionary Convergence

A stochastic process of long-term evolution due to mutation and selection is defined over an asexually reproducing population, with selection according to a population game with a one-dimensional continuity of pure strategies. Limiting the analysis to mutations of small effect, it is shown that long-term dynamic stability in such a process is equivalent to continuous stability in the relevant population game. In the case of a one-dimensional strategy set (but not necessarily if the strategy set is multi-dimensional), this result is virtually independent of the distribution of mutations.

The Evolutionary Dynamics of Selfish Replicators: a Two-level Selection Model

The aim of the present paper is to study the evolutionary dynamics of selfish replicators in a constant genetic background. Selfish replicators are viewed at a single locus, having a pleiotropic effect. Infinitely many alleles are possible; they act on individual fitness and have various levels of ability to distort segregation. This results in a two-level process of selection, including inter-individual selection (effect on individual fitness) and intra-individual selection (ability to distort segregation). The model takes other parameters into account, such as dominance, inbreeding and inbreeding depression. The system can have two different behaviours. (1) In some cases, evolutionary cycles are possible. The cycles correspond to an alternation of phases with predominant inter-individual selection, corresponding to major-effect mutations, and phases with predominant intra-individual selection, corresponding to small-effect mutations. (2) For other values of the parameters, a synthetic fitness can be defined: this absolute allelic fitness is estimated as a function of one's fitness due to both inter-individual and intra-individual selection. During the course of evolution, the synthetic fitness increases. The optimisation of a synthetic fitness is the most general process. The optimised value is essentially homologous to the value optimised for resource allocation to male and female function in hermaphrodites (female function being homologous to the effect on individual fitness, and male function being homologous to distortion ability). The relative importance of both behaviours is discussed. It is argued that repeated sequences causing some human degenerative hereditary diseases may follow a two-step evolutionary process: a progressive increase in number of sequences accompanied by a decrease of the individual fitness would be followed by massive elimination of such sequences. But in general the optimisation of the synthetic fitness seems to be more likely.

Estimate of the genomic mutation rate deleterious to overall fitness in E. coli.

Mutations are a double-edged sword: they are the ultimate source of genetic variation upon which evolution depends, yet most mutations affecting fitness (viability and reproductive success) appear to be harmful. Deleterious mutations of small effect can escape natural selection, and should accumulate in small population. Reduced fitness from deleterious-mutation accumulation may be important in the evolution of sex, mate choice, and diploid life-cycles, and in the extinction of small populations. Few empirical data exist, however. Minimum estimates of the genomic deleterious-mutation rate for viability in Drosophila melanogaster are surprisingly high, leading to the conjecture that the rate for total fitness could exceed 1.0 mutation per individual per generation. Here we use Escherichia coli to provide an estimate of the genomic deleterious-mutation rate for total fitness in a microbe. We estimate that the per-microbe rate of deleterious mutations is in excess of 0.0002.

Conditions Favoring Stable Mixed Mating Systems with Jointly Evolving Inbreeding Depression

Theory suggests that mixed mating systems can be evolutionarily stable if fitness declines monotonically with consecutive generations of self-fertilization. However, most models which assume inbreeding depression due to recessive deleterious mutations predict that inbreeding depression will be purged upon selfing, and thus will not show a monotonic decline in fitness. Fitness changes are tracked over consecutive generations of self-fertilization in a model which permits purging of load to occur. The results suggest that very mildly deleterious mutations (S = 0·01) approximate a monotonic decline in fitness within selfing lineages. This is because they are purged more slowly than the increase in homozygosity with each generation of continued selfing. The fitness functions expected at several selfing rates for mutations of small, moderate and severe effect are then calculated, assuming that purging within selfing lineages is negligible, and using this function, we predict the stable selfing rate. In several cases, the predicted stable selfing rate matches that used to calculate the fitness function, indicating that mixed mating is a stable outcome of the joint evolution of the mating system and inbreeding depression. Mixed mating is most likely when inbreeding depression is caused by partly recessive (h = 0·2-0·35) very mildly deleterious mutations with per genome mutation rates between 1·0 and 2·0. Empirical studies of mutation suggest that these parameters are not uncommon. We discuss studies of inbreeding depression which relate the selfing rate to the changes in fitness with selfing.