Is phase variation in Bordetella caused by mutation and selection?

In vitro growth conditions of Bordetella bronchiseptica led to an enrichment of phase variants. The frequency of phase variation was about 10(-6) per cell per generation. Therefore phase variation in Bordetella may result from a random mutation in a controlling region, followed by selection.     

Dilution of hypoxanthine-guanine phosphoribosyl transferase and other factors affecting the frequency of 6-thioguanine resistance in Chinese hamster lung cells.

Factors influencing the frequency of thioguanine resistant mutations were examined in Chinese hamster lung cells damaged with a carcinogen, N-acetoxy-2-acetyl aminofluorene. Factors such as inoculum density, expression time, and concentration of selective agent were found to have a profound effect on the mutation frequency.Over a range of doses, a longer expression time is required for mutant cells from a more damaged population to reach their maximum frequency. In order to investigate the elements involved in this phenomenon, the increment in the plating efficiency of treated cells as a function of expression time, spontaneous mutation rate per cell per generation, viability of mutant as well as wild type cells, and half life of HGPRTase were evaluated.There was an observed relationship between induced mutation frequency and plating efficiency of treated cells. When treated cells had recovered from effects of the treatment and arrived at the normal level of plating efficiency, they also yielded the maximum frequency of mutations.The estimated mutation rate was 5.5 × 10^?8 per cell per generation. This number is too small to account for the increment in mutation frequency with the increase in the expression time. The mutation frequency of spontaneous origin was 4 × 10^?6 and that of induction of 10^?5 M NA-AAF was 10^?4. Lower growth rates of mutant cells cannot explain this increase in the number of mutants recovered, either.Continuous diminution in the level of HGPRTase, at 35% daily, interpreted as an important factor responsible for the recovery of mutation frequency during expression time, was observed in non-dividing cells. None of a large number of mutants sampled from those isolated had HGRPT activity. This indicates that they are true mutants and are not a result of phenocopy. Only cells completely deficient in HGPRT activity are recovered in TG selection medium. It is suggested, therefore, that this cell line is suitable for mutagenicity testing in the induction of mutation at the HGPRT locus.     

Preferential mutation of the neurofibromatosis type 1 gene in paternally derived chromosomes

Summary An interesting feature of neurofibromatosis type 1 (NF1) is its high mutation rate of 1×10^–4 per gamete per generation. The molecular basis for frequent NF1 mutation in unknown; the gene is not deletion prone. We have found that in all ten families examined, the apparent new NF1 mutation occurred on the paternally-derived chromosome. The probability of observing this result by chance is less than 0.001 assuming an equal frequency of mutation of paternal and maternal NF1 genes. We hypothesize a role for genomic imprinting that may either enhance mutation of the paternal NF1 gene or confer protection from mutation to the maternal NF1 gene.     

Linkage disequilibrium, mutational analysis and natural selection in the repetitive region of the clock gene, period, in Drosophila melanogaster

We have used the method of disequilibrium pattern analysis to examine associations between the threonine-glycine (Thr-Gly) encoding repeat region of the clock gene period (per) of Drosophila melanogaster, and polymorphic sites both upstream and downstream of the repeat, in a number of European fly populations. The results are consistent with the view that selection may be operating on various haplotypes which share the Thr-Gly length alleles encoding 17, 20 and 23 dipeptide pairs, and that the repeat itself may be the focus for selection. These conclusions lend support to a number of other population and behavioural investigations which have provided evidence that selection is acting on the Thr-Gly region. The linkage analysis was also used to infer an approximate mutation rate (mu) for the repeat, of 10(-5) < mu < 4 x 10(-5) per gamete per generation. Direct measurements of the mutation rate using the polymerase chain reaction in a pedigree analysis of tens of thousands of individuals do not contradict this value. Consequently, the Thr-Gly repeat does not have a mutation rate that is as high as some of the non-coding minisatellites, but it is several orders of magnitude higher than the nucleotide substitution rate. The implications of this elevated mutation rate for linkage disequilibria and selection are discussed.     

A method to infer positive selection from marker dynamics in an asexual population

MOTIVATION: The observation of positive selection acting on a mutant indicates that the corresponding mutation has some form of functional relevance. Determining the fitness effects of mutations thus has relevance to many interesting biological questions. One means of identifying beneficial mutations in an asexual population is to observe changes in the frequency of marked subsets of the population. We here describe a method to estimate the establishment times and fitnesses of beneficial mutations from neutral marker frequency data. RESULTS: The method accurately reproduces complex marker frequency trajectories. In simulations for which positive selection is close to 5% per generation, we obtain correlations upwards of 0.91 between correct and inferred haplotype establishment times. Where mutation selection coefficients are exponentially distributed, the inferred distribution of haplotype fitnesses is close to being correct. Applied to data from a bacterial evolution experiment, our method reproduces an observed correlation between evolvability and initial fitness defect.     

Genetic instability at the adenine phosphoribosyltransferase locus in mouse L cells.

Resistance to adenine analogs such as 2,6-diaminopurine occurs at a rate of approximately 10(-3) per cell per generation in mouse L cells. This resistance is associated with a loss of detectable adenine phosphoribosyltransferase activity. Other genetic loci in L cells have the expected mutation frequency (approximately 10(-6)). Transformation of L cell mutants with Chinese hamster ovary cell DNA results in transformants with adenine phosphoribosyltransferase activity characteristic of Chinese hamster ovary cells. No activation of the mouse gene occurs on hybridization with human fibroblasts. That this high frequency event is the result of mutation rather than an epigenetic event is supported by antigenic and reversion studies of the 2,6-diaminopurine-resistant clones. These results are consistent with either a mutational hot-spot, a locus specific mutator gene, or a site of integration of an insertion sequence.     

The island model with stochastic migration

The island model with stochastically variable migration rate and immigrant gene frequency is investigated. It is supposed that the migration rate and the immigrant gene frequency are independent of each other in each generation, and each of them is independently and identically distributed in every generation. The treatment is confined to a single diallelic locus without mutation. If the diploid population is infinite, selection is absent and the immigrant gene frequency is fixed, then the gene frequency on the island converges to the immigrant frequency, and the logarithm of the absolute value of its deviation from it is asymptotically normally distributed. Assuming only neutrality, the evolution of the exact mean and variance of the gene frequency are derived for an island with finite population. Selection is included in the diffusion approximation: if all evolutionary forces have comparable roles, the gene frequency will be normally distributed at all times. All results in the paper are completely explicit.     

Rates and fitness consequences of new mutations in humans

The human mutation rate per nucleotide site per generation (μ) can be estimated from data on mutation rates at loci causing Mendelian genetic disease, by comparing putatively neutrally evolving nucleotide sequences between humans and chimpanzees and by comparing the genome sequences of relatives. Direct estimates from genome sequencing of relatives suggest that μ is about 1.1 × 10(-8), which is about twofold lower than estimates based on the human-chimp divergence. This implies that an average of ~70 new mutations arise in the human diploid genome per generation. Most of these mutations are paternal in origin, but the male:female mutation rate ratio is currently uncertain and might vary even among individuals within a population. On the basis of a method proposed by Kondrashov and Crow, the genome-wide deleterious mutation rate (U) can be estimated from the product of the number of nucleotide sites in the genome, μ, and the mean selective constraint per site. Although the presence of many weakly selected mutations in human noncoding DNA makes this approach somewhat problematic, estimates are U ≈ 2.2 for the whole diploid genome per generation and 0.35 for mutations that change an amino acid of a protein-coding gene. A genome-wide deleterious mutation rate of 2.2 seems higher than humans could tolerate if natural selection is "hard," but could be tolerated if selection acts on relative fitness differences between individuals or if there is synergistic epistasis. I argue that in the foreseeable future, an accumulation of new deleterious mutations is unlikely to lead to a detectable decline in fitness of human populations.     

Rate of deleterious mutation and the distribution of its effects on fitness in vesicular stomatitis virus

Despite their importance, the parameters describing the spontaneous deleterious mutation process have not been well described in many organisms. If mutations are important for the evolution of every living organism, their importance becomes critical in the case of RNA-based viruses, in which the frequency of mutation is orders of magnitude larger than in DNA-based organisms. The present work reports minimum estimates of the deleterious mutation rate, as well as the characterization of the distribution of deleterious mutational effects on the total fitness of the vesicular stomatitis virus (VSV). The estimates are based on mutation-accumulation experiments in which selection against deleterious mutations was minimized by recurrently imposing genetic bottlenecks of size one. The estimated deleterious mutation rate was 1.2 mutations per genome and generation, with a mean fitness effect of –0.39% per generation. At the end of the mutation-accumulation experiment, the average reduction in fitness was 38% and the distribution of accumulated deleterious effects was, on average, left-skewed. The magnitude of the skewness depends on the initial fitness of the clone analysed. The implications of our findings for the evolutionary biology of RNA viruses are discussed.     

Estimating mutation rate and generation time from longitudinal samples of DNA sequences

We present in this paper a simple method for estimating the mutation rate per site per year which also yields an estimate of the length of a generation when mutation rate per site per generation is known. The estimator, which takes advantage of DNA polymorphisms in longitudinal samples, is unbiased under a number of population models, including population structure and variable population size over time. We apply the new method to a longitudinal sample of DNA sequences of the env gene of human immunodeficiency virus type 1 (HIV-1) from a single patient and obtain 1.62 x 10(-2) as the mutation rate per site per year for HIV-1. Using an independent data set to estimate the mutation rate per generation, we obtain 1.8 days as the length of a generation of HIV-1, which agrees well with recent estimates based on viral load data. Our estimate of generation time differs considerably from a recent estimate by Rodrigo et al. when the same mutation rate per site per generation is used. Some factors that may contribute to the difference among different estimators are discussed.     

Genotypic distribution at the limits to natural and artificial selection with mutation

A general procedure for analysing the change of genotypic distributions under stabilizing and truncation selection is described here and used to investigate the genotypic distribution at the limits to selection. For comparison, a simple approximate procedure using a normal distribution is also presented. It is clear that in the long term truncation introduces departures from normality mainly through gene frequency change, rather than through the generation of linkage disequilibrium under random mating. The Gaussian approximation performs reasonably well for additive gene effects unless the mean gene frequency is very extreme (say, outside the range of 0.05 to 0.95) and the number of loci is small (say, less then 50) regardless of the type of selection in operation. The genotypic distribution at the limits to selection largely depends on the type of limit reached. If a limit is obtained due to the action of natural selection before the exhaustion of existing variation, the distribution will normally not be very skew, but if a limit is reached at which mutation plays a central role in the maintenance of genetic variability, it could have high coefficients of skewness and kurtosis. The role of mutation on the long-term response is also discussed.     

The mutational load of a multigene family with uniform members

The mutational load of a multigene family with uniform members was studied by computer simulations. Two models of selection, truncation and exponential fitness, were examined, by using a simple model of gene conversion. It was found that the load is much smaller than the Haldane-Muller prediction under the truncation selection, and that it becomes approximately equal to the value calculated by the formula, nv(1-q)/(m-nq), where n is the copy number, v is the rate of detrimental mutation per gene copy, m is the truncation point in terms of the number of detrimental genes eliminated, and q is the equilibrium frequency of detrimental mutation. However the equilibrium frequency cannot be analytically obtained. For the exponential fitness model, the load is close to the Haldane-Muller value. When there is no gene conversion, the load becomes larger than the cases with conversion both for the truncation and the exponential fitness models. Thus, gene conversion or other mechanisms that are responsible for contraction-expansion of mutants on chromosomes helps eliminating deleterious mutations occurring in multigene families.     

On an extremum principle in the genetical theory of natural selection

Natural selection causes gene frequency changes in a large population leading to genetic evolution over evolutionary time scales. Such gene frequency changes, however, involve an optimizing principle. According to Kimura, such changes, over a short interval of time, occur in a manner such that the increase in population fitness is maximum for a given distance between parent and daughter generation gene frequencies. But according to Ewens, of all gene frequency changes, including those that lead to the same partial increase in mean fitness as the natural selection gene frequency changes, the natural selection values minimize the generalized distance measure between parent and daughter generation gene frequency values. These two optimality principles happen to be mirror images of each other. However, the optimality principles are restricted to the case where the increase in mean fitness is to thefirst order in natural selection gene frequency changes. I show in this paper that, instead of linear approximation to the increase in mean fitness, the treatment can be fairly general, and the exact increase in mean fitness can be considered so as to include the dominance effects of the genes.     

Estimation of Mutation Rates Based on the Analysis of Polypeptide Constituents of Cultured Human Lymphoblastoid Cells

A subclone of a human diploid lymphoblastoid cell line, TK-6, with consistently high cloning efficiency has been used to estimate the rates of somatic mutations on the basis of protein variation detected by two-dimensional polyacrylamide gel electrophoresis. A panel of 267 polypeptide spots per gel was screened, representing the products of approximately 263 unselected loci. The rate of human somatic mutation in vitro was estimated by measuring the proportion of protein variants among cell clones isolated at various times during continuous exponential growth of a TK-6 cell population. Three mutants of spontaneous origin were observed, giving an estimated spontaneous rate of 6 x 10(-8) electrophoretic mutations per allele per cell generation (i.e., 1.2 x 10(-7) per locus per cell generation). Following treatment of cells with N-ethyl-N-nitrosourea, a total of 74 confirmed variants at 54 loci were identified among 1143 clones analyzed (approximately 601,000 allele tests). The induced variants include 65 electromorphs which exhibit altered isoelectric charge and/or apparent molecular weight and nine nullimorphs for each of which a gene product was not detected at its usual location on the gel. The induced frequency for these 65 structural gene mutants is 1.1 x 10(-4) per allele. An excess of structural gene mutations at ten known polymorphic loci and repeat mutations at these and other loci suggest nonrandomness of mutation in human somatic cells. Nullimorphs occurring at three heterozygous loci in TK-6 cells may be caused by genetic processes other than structural gene mutation.     

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.     

Life history and the male mutation bias

Abstract If DNA replication is a major cause of mutation, then those life-history characters, which are expected to affect the number of male germline cell divisions, should also affect the male to female mutation bias (a_m). We tested this hypothesis by comparing several clades of bird species, which show variation both in suitable life-history characters (generation time as measured by age at first breeding and sexual selection as measured by frequency of extrapair paternity) and in a_m, which was estimated by comparing Z-linked and W-linked substitution rates in gametologous introns. a_m differences between clades were found to positively covary with both generation time and sexual selection, as expected if DNA replication causes mutation. The effects of extrapair paternity frequency on a_m suggests that increased levels of sexual selection cause higher mutation rates, which offers an interesting solution to the paradox of the loss of genetic variance associated with strong directional sexual selection. We also used relative rate tests to examine whether the observed differences in a_m between clades were due to differences in W-linked or Z-linked substitution rates. In one case, a significant difference in a_m between two clades was shown to be due to W-linked rates and not Z-linked rates, a result that suggests that mutation rates are not determined by replication alone.     

Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates

The rate at which human genomes mutate is a central biological parameter that has many implications for our ability to understand demographic and evolutionary phenomena. We present a method for inferring mutation and gene-conversion rates by using the number of sequence differences observed in identical-by-descent (IBD) segments together with a reconstructed model of recent population-size history. This approach is robust to, and can quantify, the presence of substantial genotyping error, as validated in coalescent simulations. We applied the method to 498 trio-phased sequenced Dutch individuals and inferred a point mutation rate of 1.66 × 10⁻⁸ per base per generation and a rate of 1.26 × 10⁻⁹ for <20 bp indels. By quantifying how estimates varied as a function of allele frequency, we inferred the probability that a site is involved in non-crossover gene conversion as 5.99 × 10⁻⁶. We found that recombination does not have observable mutagenic effects after gene conversion is accounted for and that local gene-conversion rates reflect recombination rates. We detected a strong enrichment of recent deleterious variation among mismatching variants found within IBD regions and observed summary statistics of local sharing of IBD segments to closely match previously proposed metrics of background selection; however, we found no significant effects of selection on our mutation-rate estimates. We detected no evidence of strong variation of mutation rates in a number of genomic annotations obtained from several recent studies. Our analysis suggests that a mutation-rate estimate higher than that reported by recent pedigree-based studies should be adopted in the context of DNA-based demographic reconstruction.     

On the Organization of Higher Chromosomes

OHTA and Kimura¹ have argued that only about 6% of the sequences in mammalian DNA can be under the intense selection that has characterized the evolutionary history of the cytochromes c, the globin chains and the histones. From the calculated mutation rate of fibrinopeptides A and B they show that if all genes are subjected to the same mutation rate 8.3 mutations would accumulate per genome per generation. Because 0,5 deleterious mutations per genome per generation is the maximum allowable in an equilibrium population², they conclude that the amount of DNA that codes for informational sequences such as the cytochromes, globins and histones must be no more than 0.5/8.3, or 6%. We are therefore left with the interesting observation that 94% of mammalian nuclear DNA serves a function not under strong selection. These authors make several assumptions, one of which is that the spontaneous mutation rate characteristic of a species is constant over all nucleotide sequences. I suggest here that this assumption is incorrect, for a variety of reasons and that by assuming that spontaneous mutation rates vary sequence by sequence, one can arrive at a plausible organizing principle for the structure of higher chromosomes.     

Selection and mutation at a diallelic X-linked locus

Equilibria and convergence of gene frequencies are studied in the case of a diallelic X-linked locus under the influence of selection and mutation. The model used is that of an infinite diploid population with nonoverlapping discrete generations and random mating. It is proved that if the mutation rates and fitnesses are constant and the mutation rates are less than one-third, then global convergence of gene frequencies to equilibria occurs. The phase portraits of the dynamical system describing the change of allelic frequencies from one generation to the next are determined. Convergence of gene frequencies is monotone from a certain generation on if every other generation is skipped. In the case without mutation, our proof of this monotone convergence simplifies G. Palm's original proof [37].     

Social selection in human populations. I. Modification of the fitness of offspring by an affected parent.

The concept of social selection for deleterious genes has been introduced by considering two alleles at one locus. A social selection model is constructed by assuming that the fitness of an individual is determined by his or her own as well as the parental phenotypes. It is shown that the equilibrium gene frequency depends on the loss of fitness of an individual due to the trait (gamma), due to affected parents (beta), and the probability that the heterozygote develops the trait (h). With mutational changes from the wild-type allele to the deleterious gene at a rate of alpha per generation, the equilibrium frequency of deleterious genes is approximately alpha/hs for 0 less than h less than or equal to 1 and square root alpha/s for h = 0, where s = gamma + beta(1 -- gamma)/2. Implications of the social selection model have been discussed for several diseases in man.