Showing papers on "Mutation rate published in 1993"
TL;DR: From these properties, several new statistical tests based on a random sample of DNA sequences from the population are developed for testing the hypothesis that all mutations at a locus are neutral.
Abstract: Mutations in the genealogy of the sequences in a random sample from a population can be classified as external and internal. External mutations are mutations that occurred in the external branches and internal mutations are mutations that occurred in the internal branches of the genealogy. Under the assumption of selective neutrality, the expected number of external mutations is equal to theta = 4Ne mu, where Ne is the effective population size and mu is the rate of mutation per gene per generation. Interestingly, this expectation is independent of the sample size. The number of external mutations is likely to deviate from its neutral expectation when there is selection while the number of internal mutations is less affected by the presence of selection. Statistical properties of the numbers of external mutations and of internal mutations are studied and their relationships to two commonly used estimates of theta are derived. From these properties, several new statistical tests based on a random sample of DNA sequences from the population are developed for testing the hypothesis that all mutations at a locus are neutral.
3,880 citations
TL;DR: It is shown that 12 per cent of colorectal carcinomas carry somatic deletions in poly(dA . dT) sequences and other simple repeats, and it is concluded that these mutations reflect a previously undescribed form of carcinogenesis in the colon mediated by a mutation in a DNA replication factor resulting in reduced fidelity for replication or repair (a 'mutator mutation').
Abstract: Spontaneous errors in DNA replication have been suggested to play a significant role in neoplastic transformation and to explain the chromosomal alterations seen in cancer cells. A defective replication factor could increase the mutation rate in clonal variants arising during tumour progression, but despite intensive efforts, increases in tumour cell mutation rates have not been unambiguously shown. Here we use an unbiased genomic fingerprinting technique to show that 12 per cent of colorectal carcinomas carry somatic deletions in poly(dA.dT) sequences and other simple repeats. We estimate that cells from these tumours can carry more than 100,000 such mutations. Only tumours with affected poly(dA.dT) sequences carry mutations in the other simple repeats examined, and such mutations can be found in all neoplastic regions of multiple tumours from the same patient, including adenomas. Tumours with these mutations show distinctive genotypic and phenotypic features. We conclude that these mutations reflect a previously undescribed form of carcinogenesis in the colon (predisposition to which may be inherited) mediated by a mutation in a DNA replication factor resulting in reduced fidelity for replication or repair (a 'mutator mutation').
2,724 citations
TL;DR: Analytical theory shows that there is a simple relationship between M̂ and geographic distance in both equilibrium and non‐equilibrium populations and that this relationship is approximately independent of mutation rate when the mutation rate is small.
Abstract: It is shown that for allele frequency data a useful measure of the extent of gene flow between a pair of populations is M∘=(1/FST-1)/4, which is the estimated level of gene flow in an island model at equilibrium. For DNA sequence data, the same formula can be used if FST is replaced by NST . In a population with restricted dispersal, analytic theory shows that there is a simple relationship between M and geographic distance in both equilibrium and non-equilibrium populations and that this relationship is approximately independent of mutation rate when the mutation rate is small. Simulation results show that with reasonable sample sizes, isolation by distance can indeed be detected and that, at least in some cases, non-equilibrium patterns can be distinguished. This approach to analyzing isolation by distance is used for two allozyme data sets, one from gulls and one from pocket gophers.
2,499 citations
TL;DR: Observed reductions in molecular variation in low recombination genomic regions of sufficiently large size, for instance in the centromere-proximal regions of Drosophila autosomes or in highly selfing plant populations, may be partly due to background selection against deleterious mutations.
Abstract: Selection against deleterious alleles maintained by mutation may cause a reduction in the amount of genetic variability at linked neutral sites. This is because a new neutral variant can only remain in a large population for a long period of time if it is maintained in gametes that are free of deleterious alleles, and hence are not destined for rapid elimination from the population by selection. Approximate formulas are derived for the reduction below classical neutral values resulting from such background selection against deleterious mutations, for the mean times to fixation and loss of new mutations, nucleotide site diversity, and number of segregating sites. These formulas apply to random-mating populations with no genetic recombination, and to populations reproducing exclusively asexually or by self-fertilization. For a given selection regime and mating system, the reduction is an exponential function of the total mutation rate to deleterious mutations for the section of the genome involved. Simulations show that the effect decreases rapidly with increasing recombination frequency or rate of outcrossing. The mean time to loss of new neutral mutations and the total number of segregating neutral sites are less sensitive to background selection than the other statistics, unless the population size is of the order of a hundred thousand or more. The stationary distribution of allele frequencies at the neutral sites is correspondingly skewed in favor of rare alleles, compared with the classical neutral result. Observed reductions in molecular variation in low recombination genomic regions of sufficiently large size, for instance in the centromere-proximal regions of Drosophila autosomes or in highly selfing plant populations, may be partly due to background selection against deleterious mutations.
1,807 citations
TL;DR: A total of 20,000 parent-offspring transfers of alleles were examined through the genotyping within 40 CEPH reference families of 28 short tandem repeat polymorphisms (STRPs) located on chromosome 19, and the average mutation rate was nearly four times higher than the average rate for dinucleotide STRPs.
Abstract: A total of 20,000 parent-offspring transfers of alleles were examined through the genotyping within 40 CEPH reference families of 28 short tandem repeat polymorphisms (STRPs) located on chromosome 19. Forty-seven initial mutation events were detected in the STRPs using DNA from transformed lymphoblastoid cell lines, but less than half (39%) could be verified using DNA from untransformed cells. None of the cases where three alleles were observed in a single individual could be verified using DNA from untransformed cells. The average mutation rate for the chromosome 19 STRPs after correction for events which would not be detectable as Mendelian errors was 1.2 x 10(-3) per locus per gamete per generation. This rate may have been inflated by somatic as opposed to germline events. Observed mutation rates for individual STRPs ranged from 0 to 8 x 10(-3). The average mutation rate for tetranucleotide STRPs was nearly four times higher than the average rate for dinucleotide STRPs. For determination of the mode of mutation, events involving STRPs on other chromosomes were also examined. Of the events which were verified using DNA from untransformed lymphocytes or which were likely among those for which DNA from untransformed cells was not available: none were located at the sites of meiotic recombination, 91% involved the gain or loss of a single repeat unit, and 15 occurred in the male germline compared to 4 in the female germline (p = 0.01).
1,580 citations
TL;DR: Reconsideration of the generation time hypothesis to include physiological effects such as metabolic rate improves the theoretical underpinnings of molecular evolution.
Abstract: There is increasing evidence for variation in rates of nucleotide substitution among divergent taxonomic groups. Here, we summarize published rate data and show a strong relationship between substitution rate and body size. For instance, rates of nuclear and mtDNA evolution are slow in whales, intermediate in primates, and fast in rodents. A similar relationship exists for poikilothermic vertebrates. However, these taxa have slower mtDNA substitution rates overall than do homeotherms of similar size. A number of physiological and life history variables are highly correlated with body size. Of these, generation time and metabolic rate explain some patterns of rate heterogeneity equally well. In many cases, however, differences in metabolic rate explain important exceptions to the generation time model. Correlation between metabolic rate and nucleotide substitution may be mediated by (i) the mutagenic effects of oxygen radicals that are abundant by-products of aerobic respiration, and (ii) increased rates of DNA synthesis and nucleotide replacement in organisms with higher metabolic rates. Both of these factors increase mutation rate by decreasing the "nucleotide generation time," the average length of time before a nucleotide is copied either through replication or repair. Reconsideration of the generation time hypothesis to include physiological effects such as metabolic rate improves the theoretical underpinnings of molecular evolution.
1,151 citations
TL;DR: There is a clear central tendency for lytic RNA viruses to display rates of spontaneous mutation of approximately 1 per genome per replication, which is some 300-fold higher than previously reported for DNA-based microbes.
Abstract: Simple methods are presented to estimate rates of spontaneous mutation from mutant frequencies and population parameters in RNA viruses. Published mutant frequencies yield a wide range of mutation rates per genome per replication, mainly because mutational targets have usually been small and, thus, poor samples of the mutability of the average base. Nevertheless, there is a clear central tendency for lytic RNA viruses (bacteriophage Q beta, poliomyelitis, vesicular stomatitis, and influenza A) to display rates of spontaneous mutation of approximately 1 per genome per replication. This rate is some 300-fold higher than previously reported for DNA-based microbes. Lytic RNA viruses thus mutate at a rate close to the maximum value compatible with viability. Retroviruses (spleen necrosis, murine leukemia, Rous sarcoma), however, mutate at an average rate about an order of magnitude lower than lytic RNA viruses.
729 citations
TL;DR: There is no correlation between the mean and variance in allele size at a locus or between the number of alleles and mean allele size, which suggests that the mutation rate at these loci is independent of allele size.
Abstract: We summarize available data on the frequencies of alleles at microsatellite loci in human populations and compare observed distributions of allele frequencies to those generated by a simulation of the stepwise mutation model. We show that observed frequency distributions at 108 loci are consistent with the results of the model under the assumption that mutations cause an increase or decrease in repeat number by one and under the condition that the product Nu, where N is the effective population size and u is the mutation rate, is larger than one. We show that the variance of the distribution of allele sizes is a useful estimator of Nu and performs much better than previously suggested estimators for the stepwise mutation model. In the data, there is no correlation between the mean and variance in allele size at a locus or between the number of alleles and mean allele size, which suggests that the mutation rate at these loci is independent of allele size.
608 citations
TL;DR: It is shown that the genetic context in which a mutation occurs can play a significant role in determining the type of illness produced, and this work proves that CFTR variants that alter splicing efficiency of exon 9 can affect phenotype.
Abstract: Cystic fibrosis (CF) is caused by mutations in the CF transmembrane conductance regulator (CFTR) gene but the association between mutation (genotype) and disease presentation (phenotype) is not straightforward. We have been investigating whether variants in the CFTR gene that alter splicing efficiency of exon 9 can affect the phenotype produced by a mutation. A missense mutation, R117H, which has been observed in three phenotypes, was found to occur on two chromosome backgrounds with intron 8 variants that have profoundly different effects upon splicing efficiency. A close association is shown between chromosome background of the R117H mutation and phenotype. These findings demonstrate that the genetic context in which a mutation occurs can play a significant role in determining the type of illness produced.
435 citations
Proceedings Article•
01 Jun 1993
TL;DR: The results indicate that a variation of the mutation rate is useful in cases where the tness function is a multimodal pseudo boolean function where multimodality may be caused by the objective function as well as the encoding mechanism.
Abstract: The optimization of a single bit string by means of iterated mutation and selection of the best a Genetic Algorithm is dis cussed with respect to three simple tness functions The counting ones problem a standard binary encoded integer and a Gray coded integer optimization problem A mu tation rate schedule that is optimal with re spect to the success probability of mutation is presented for each of the objective functions and it turns out that the standard binary code can hamper the search process even in case of unimodal objective functions While normally a mutation rate of l where l de notes the bit string length is recommend able our results indicate that a variation of the mutation rate is useful in cases where the tness function is a multimodal pseudo boolean function where multimodality may be caused by the objective function as well as the encoding mechanism
409 citations
TL;DR: The Mhc genes are found to evolve at a relatively slow rate with the regularity of a clock and the nonsynonymous sites coding for the peptide-binding region (PBR) are under moderate negative selection pressure.
Abstract: In the last few years, more than 500 primate major histocompatibility complex (Mhc) genes or parts thereof have been sequenced. The extraordinary sequence information is used here to draw conclusions about the manner of Mhc evolution. The Mhc genes are found to evolve at a relatively slow rate with the regularity of a clock. It takes from 1 to 6 million years for a new mutation to be incorporated into an Mhc allele, and the mutation rate is comparable to that of most other primate genes. The nonsynonymous sites coding for the peptide-binding region (PBR) are under relatively weak positive selection pressure (selection coefficient of a few percent only); the nonsynonymous non-PBR sites are under moderate negative selection pressure. The positive pressure is probably provided by parasites and is responsible for the trans-species persistence of allelic lineages at functional Mhc loci for more than 40 million years.
TL;DR: Analytical models for mutation accumulation that obviate the need for time‐consuming computer simulations in certain ranges of the parameter space are developed and it is shown that an intermediate selection coefficient minimizes the time to extinction.
Abstract: We extend our earlier work on the role of deleterious mutations in the extinction of obligately asexual populations. First, we develop analytical models for mutation accumulation that obviate the need for time-consuming computer simulations in certain ranges of the parameter space. When the number of mutations entering the population each generation is fairly high, the number of mutations per individual and the mean time to extinction can be predicted using classical approaches in quantitative genetics. However, when the mutation rate is very low, a fixation-probability approach is quite effective. Second, we show that an intermediate selection coefficient (s) minimizes the time to extinction. The critical value of s can be quite low, and we discuss the evolutionary implications of this, showing that increased sensitivity to mutation and loss of capacity for DNA repair can be selectively advantageous in asexual organisms. Finally, we consider the consequences of the mutational meltdown for the extinction of mitochondrial lineages in sexual species.
TL;DR: The effects of breeding system and rate of recombination on the rate of molecular evolution by the fixation of slightly deleterious alleles are discussed and the effects of differences in the selection parameters (strength of selection, dominance coefficient), of multiplicative versus synergistic selection, and of different amounts of inbreeding are investigated.
Abstract: We have carried out an investigation of the effects of various parameters on the accumulation of deleterious mutant alleles in finite diploid populations. Two different processes contribute to mutation accumulation. In random-mating populations of very small size and with tight linkage, fixation of mutant alleles occurs at a high rate, but decreases with extremely tight linkage. With very restricted recombination, the numbers of low-frequency mutant alleles per genome in randommating populations increase over time independently of fixation (Muller's ratchet). Increased population size affects the ratchet less than the fixation process, and the decline in population fitness is dominated by the ratchet in populations of size greater than about 100, especially with high mutation rates. The effects of differences in the selection parameters (strength of selection, dominance coefficient), of multiplicative versus synergistic selection, and of different amounts of inbreeding, are complex, but can be interpreted in terms of opposing effects of selection on individual loci and associations between loci. Stronger selection slows the accumulation of mutations, though a faster decline in mean fitness sometimes results. Increasing dominance tends to have a similar effect to greater strength of selection. High inbreeding slows the ratchet, because the increased homozygous expression of mutant alleles in inbred populations has effects similar to stronger selection, and because with inbreeding there is a higher initial frequency of the least loaded class. Fixation of deleterious mutations is accelerated in highly inbred populations. Even with inbreeding, sexual populations larger than 100 will probably rarely experience mutation accumulation to the point that their survival is endangered because neither fixation nor the ratchet has effects of the magnitude seen in asexual populations. The effects of breeding system and rate of recombination on the rate of molecular evolution by the fixation of slightly deleterious alleles are discussed.
TL;DR: It is proposed that the POL3 3′‐‐>)5′ exonuclease and the PMS1 mismatch repair system act on a common pathway analogous to the dnaQ‐‐>mutHLS pathway of DNA replication error correction in Escherichia coli.
Abstract: Mutation of predicted 3'-->5' exonuclease active site residues of Saccharomyces cerevisiae POL3 DNA polymerase (delta) or deletion of the PMS1 mismatch repair gene lead to relative (to wild type) spontaneous mutation rates of approximately 130 and 41, respectively, measured at a URA3 reporter gene inserted near to a defined replication origin. The POL3 exonuclease-deficient mutant pol3-01 generated most classes of single base mutation in URA3, indicating a broad specificity that generally corresponds to that of the PMS1 system. pol3-01 pms1 haploid cells ceased growth after a few divisions with no unique terminal cell morphology. A pol3-01/pol3-01 pms1/pms1 diploid was viable and displayed an estimated URA3 relative mutation rate of 2 x 10(4), which we calculate to be catastrophically high in a haploid. The relationship between the relative mutation rates of pol3-01 and pms1 was multiplicative, indicating action in series. The PMS1 transcript showed the same cell cycle periodicity as those of a set of DNA replication genes that includes POL3, suggesting PMS1 is co-regulated with these genes. We propose that the POL3 3'-->5' exonuclease and the PMS1 mismatch repair system act on a common pathway analogous to the dnaQ-->mutHLS pathway of DNA replication error correction in Escherichia coli.
TL;DR: The estimate of αm supports the view that the evolution of DNA sequences in higher primates is male-driven and is, however, much lower than the previous estimate and therefore raises a number of issues.
Abstract: It is commonly believed that the mutation rate is much higher in the human male germ line than in the female germ line because the number of germ-cell divisions per generation is much larger in males than in females. But direct estimation of mutation rates is difficult, relying mainly on sex-linked genetic diseases, so the ratio (alpha m) of male to female mutation rates is not clear. It has been noted that if alpha m is very large, then the rate of synonymous substitution in X-linked genes should be only 2/3 of that in autosomal genes, and comparison of human and rodent genes supported this prediction. As the number of X-linked genes used in the study was small and the X-linked and autosomal sequences were non-homologous, and given that the synonymous rate varies among genes, we sequenced the last intron (approximately 1 kb) of the Y-linked and X-linked zinc-finger-protein genes (ZFY and ZFX) in humans, orang-utans, baboons and squirrel monkeys. The ratio Y/X of the substitution rate in the Y-linked intron to that in the X-linked intron is approximately 2.3, which is close to that estimated from synonymous rates in the ZFY and ZFX genes and implies alpha m approximately 6. This estimate of alpha m supports the view that the evolution of DNA sequences in higher primates is male-driven. It is, however, much lower than the previous estimate and therefore raises a number of issues.
TL;DR: One hundred ninety‐four consecutive primary, recurrent, and metastatic colorectal adenocarcinomas, accessioned during 1991 at Rhode Island Hospital, were classified according to the presence and specific type of K‐ras‐2 point mutation.
Abstract: Background. New measures enabling better prediction of biologic behavior of large bowel cancer are highly desirable. One hundred ninety-four consecutive primary, recurrent, and metastatic colorectal adenocarcinomas, accessioned during 1991 at Rhode Island Hospital, were classified according to the presence and specific type of K-ras-2 point mutation.
Methods. An integrated histopathologic-genetic approach was used to detect mutations starting with minute, topographically selected, tissue samples from formaldehyde-fixed, paraffin-embedded specimens.
Results. Each colorectal adenocarcinoma exhibited either no or only one of seven specific types of K-ras-2 mutation. The mutation type of each primary tumor was present consistently in its metastatic deposits. Thirtyfive percent of primary colorectal adenocarcinomas were found to be mutated (42 of 119). A significantly higher mutation rate (65%) was seen in lymphogenous-hematogenous metastases as a group (35 of 54; P < 0.005). By contrast, 22% of anastomotic recurrences and transcoelomic metastasis were mutated (4 of 18). Twenty-eight percent of adenocarcinomas with invasion limited to muscularis propria (Tis, T1, T2) were mutated (16 of 57), compared to 41% for more deeply invasive tumors (T3, T4; 26 of 63). When colorectal adenocarcinomas were analyzed by specific K-ras-2 mutation type, it was found that codon 13 mutated tumors did not progress to local or distant metastasis (P < 0.01). Tumors having a codon 12 valine substitution did not metastasize beyond pericolonic-perirectal lymph nodes. In contrast, colorectal cancers with codon 12 aspartic acid substitutions accounted for most of the distant hematogenous deposits (P < 0.01). Tumors with normal K-ras-2 accounted for most intraperitoneal deposits.
Conclusions. Genotyping of colorectal adenocarcinoma by K-ras-2 status can identify subsets of patients likely to pursue indolent and aggressive forms of disease. The integrated histopathologic-genetic approach outlined is feasible for use in diagnostic pathology, providing information that together with clinicopathologic staging may individualize and optimize treatment.
TL;DR: Evidence is presented that minisatellite mutation rate in mice is increased by low doses of ionizing radiation, which is useful for detecting induced mutations in relatively small samples.
Abstract: The detection of changes in germline mutation rate in human populations remains extremely difficult. Estimating the genetic hazards of radiation and other mutagens in humans therefore depends on extrapolation from experimental systems. Because of the very low frequency of spontaneous mutation at most loci, enormous samples are required to detect increases of mutation rate. A very high rate of spontaneous germline mutation altering the length of minisatellite loci has been found in human populations and therefore this system might be useful for detecting induced mutations in relatively small samples. Here we present evidence that minisatellite mutation rate in mice is increased by low doses of ionizing radiation.
TL;DR: It is argued that there is a decrease in the frequency of A, and an increase in thefrequency of G along the E.coli genes at all three codon positions, which are most consistent with selection to avoid mRNA secondary structure.
Abstract: It has been shown previously that the synonymous substitution rate between Escherichia coli and Salmonella typhimurium is lower in highly than in weakly expressed genes, and it has been suggested that this is due to stronger selection for translational efficiency in highly expressed genes as reflected in their greater codon usage bias. This hypothesis is tested here by comparing the substitution rate in codon families with different patterns of synonymous codon use. It is shown that the decline in the substitution rate across expression levels is as great for codon families that do not appear to be subject to selection for translational efficiency as for those that are. This implies that selection on translational efficiency is not responsible for the decline in the substitution rate across genes. It is argued that the most likely explanation for this decline is a decrease in the mutation rate. It is also shown that a simple evolutionary model in which synonymous codon use is determined by a balance between mutation, selection for an optimal codon, and genetic drift predicts that selection should have little effect on the substitution rate in the present case.
TL;DR: The results show that the optimum mutation schedule is one with brief bursts of high mutation rates interspersed between periods of mutation-free growth, and this model provides a framework within which the anatomy and kinetics of the germinal center reaction can be understood.
TL;DR: The age of the father is the main factor determining the human spontaneous mutation rate, and probably the total mutation rate.
Abstract: The much larger number of cell divisions between zygote and sperm than between zygote and egg, the increased age of fathers of children with new dominant mutations, and the greater evolution rate of pseudogenes on the Y chromosome than of those on autosomes all point to a much higher mutation rate in human males than in females, as first pointed out by Haldane [Ann Eugen 13:262–271, 1947] in his classical study of X-linked hemophilia. The age of the father is the main factor determining the human spontaneous mutation rate, and probably the total mutation rate.
The total mutation rate in Drosophila males of genes causing minor reduction in viability is at least 0.4 per sperm, and may be considerably higher. The great mutation load implied by a rate of ≈ 1 per zygote can be greatly ameliorated by quasi-truncation selection.
Corresponding data are not available for the human population. The evolution rate of pseudogenes in primates suggests some 102 new mutations per zygote. Presumably the overwhelming majority of these are neutral, but even the approximate fraction is not known.
Statistical evidence in Drosophila shows that mutations with minor effects cause about the same heterozygous impairment of fitness as those that are lethal when homozygous. The magnitude of heterozygous effect is such that almost all mutant genes are eliminated as heterozygotes before ever becoming homozygous. Although quantitative data in the human species are lacking, anecdotal information supports the conclusion that partial dominance is the rule here as well. This suggests that if the human mutation rate were increased or decreased, the effects would be spread over a period of 50–100 generations. © 1993 Wiley-Liss, Inc.
TL;DR: A method of measuring the human genomic deleterious mutation rate based on comparison of the rate of evolution per nucleotide per generation of neutral sequences, μN, with the overall rate of Evolution of unique sequence DNA, μo is proposed.
Abstract: We propose a method of measuring the human genomic deleterious mutation rate based on comparison of the rate of evolution per nucleotide per generation of neutral sequences, microN, with the overall rate of evolution of unique sequence DNA, microO. Data on microN, which are based on pseudogenes, permit an estimate of the total zygotic (twice the genomic) mutation rate, UT = 2 microNn = 2(2 x 10(-8)(3 x 10(9)) approximately 10(2), where n is the number of nucleotides per genome. Data on microO can be obtained by comparison of representative samples of relatively short homologous sequences from the genomes of Homo and a related species. The fraction of the genome that is controlled by negative selection is fS = (microN - microO)/microN and the deleterious zygotic mutation rate, the expected number of new deleterious alleles carried by a zygote, is US = UTfS. If fS > 0.01, US > 1, which would have important implications for human genetics and evolutionary biology.
TL;DR: Microsatellite allele variability associated with delta F508, G542X and N1303K demonstrates that slippage and mispairing is the main mechanism generating microsatellite alleles.
Abstract: Highly informative intragenic microsatellite markers within the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) gene allow the analysis of associations between specific mutations and haplotypes. We have analysed 440 Spanish CF families carrying 22 different CF mutations and have established haplotypes in 1,036 chromosomes for microsatellites IVS8CA, IVS17BTA and IVS17BCA. No new alleles were detected at the three CFTR microsatellites, in more than 3,000 meiosis analysed (estimated mutation rate of less than 3.3 x 10(-4)). The evolution of 16 haplotypes associated with the most common CF mutation, delta F508, and the low mutation rate at these microsatellite loci suggest that delta F508 originated within the 23-31-13 haplotype at least 53,000 years ago, very early in the history of the European population. The number of haplotype changes seen for two other common mutations, G542X (haplotype 23-33-13) and N1303K (23-31-13), suggests that they originated at least 35,000 years ago. Microsatellite allele variability associated with delta F508, G542X and N1303K demonstrates that slippage and mispairing is the main mechanism generating microsatellite alleles. In spite of the haplotype variability detected for these 3 common mutations, the association between haplotype and mutations is very strong. Mutations 1609delCA, 3667del4, delta I507 and G551D are all associated with haplotype 16-7-17, which has a frequency of 14.5% in normal chromosomes. 5 haplotypes bearing specific CF mutations were not found in normal chromosomes. Haplotype 16-46-13 is strongly associated with CF mutations E92K and 3601-111G-->C. About 23% of CF chromosomes with unknown mutations show significant linkage disequilibrium for microsatellite haplotypes.(ABSTRACT TRUNCATED AT 250 WORDS)
Journal Article•
TL;DR: The response does not appear to be dependent upon the occurrence of a rare Ig gene rearrangement or specific somatic mutation, and in individual mice is oligoclonal, suggestive of Ag selection.
Abstract: Anti-Sm autoantibodies are unique to SLE, but are present in only 25% of patients with this disease. This response also occurs at a similar frequency in mice of the autoimmune MRL strains. Previous analyses of the anti-Sm response in these mice indicate that its occurrence is controlled by stochastic events, and suggest that Sm is the driving Ag. To further elucidate the role of Ag in this response, and to test the hypothesis that the 25% incidence is due to a requirement for particular Ig gene rearrangements or somatic mutations, we have analyzed the specificity and V-region gene sequences of 41 anti-Sm B cell hybridomas derived from nine anti-Sm-positive MRL/Mp-lpr/lpr mice. The majority of hybridomas are specific for the D peptide of the Sm particle. Hybridomas of independent origin express unique VH/V kappa combinations with diverse junctional sequences and are variable in the extent of somatic mutation. Thus, the response does not appear to be dependent upon the occurrence of a rare Ig gene rearrangement or specific somatic mutation. The response exhibits restriction in JH and VH gene use, and in individual mice is oligoclonal, suggestive of Ag selection. In the few B cells for which mutations can be identified, the evidence for selection of mutant B lymphocytes, based on patterns of mutation, is ambiguous. However, there is remarkably little intraclonal diversity, suggesting that the overall mutation rates in these clones are low.
TL;DR: Despite the extraordinary polymorphism, the mutation rate at the primate MHC loci is no higher than that of other loci, and the Dm-based method nearly always has the highest probability of recovering true rates, provided that Dm is not smaller than 5.
Abstract: Because the divergence of many allelic lineages at the major histocompatibility complex (MHC) loci predates species divergence, standard methods of calculating synonymous substitution rates are not applicable to this system. We used three alternative methods of rate estimation: one based on the minimum number of substitutions (Dm), another on the nucleotide difference (Dxy), and the third on the net nucleotide difference (Dn). We applied these methods to the protein-encoding sequences of primate MHC class I (A, B, and C) and class II (DRB1) genes. To determine the reliability of the different estimates, we carried out computer simulation. The distribution of the estimates based on Dxy or Dn is generally much broader than that based on Dm. More importantly, the Dm-based method nearly always has the highest probability of recovering true rates, provided that Dm is not smaller than 5. Because of its desirable statistical properties, we used the Dm-based method to estimate the rate of synonymous substitutions. The rate is 1.37 +/- 0.61 for A, 1.84 +/- 0.40 for B, 3.87 +/- 1.05 for C, and 1.18 +/- 0.36 for DRB1 loci, always per site per 10(9) years. Hence despite the extraordinary polymorphism, the mutation rate at the primate MHC loci is no higher than that of other loci.
Journal Article•
TL;DR: Analysis of the factor IX gene of 260 consecutive families with hemophilia B suggests that germ-line mutations are associated with a small increase in parental age in females but little, if any, increase in males, and biases in the present data result in an underestimate of the enhancement of mutation in males.
Abstract: Previous epidemiological and biochemical studies have generated conflicting estimates of the sex ratio of mutation. Direct genomic sequencing in combination with haplotype analysis extends previous analyses by allowing the precise mutation to be determined in a given family. From analysis of the factor IX gene of 260 consecutive families with hemophilia B, we report the germ-line origin of mutation in 25 families. When combined with 14 origins of mutation reported by others and with 4 origins previously reported by us, a total of 25 occur in the female germ line, and 18 occur in the male germ line. The excess of germ-line origins in females does not imply an overall excess mutation rate per base pair in the female germ line. Bayesian analysis of the data indicates that the sex ratio varies with the type of mutation. The aggregate of single-base substitutions shows a male predominance of germ-line mutations (P < .002). The maximum-likelihood estimate of the male predominance is 3.5-fold. Of the single-base substitutions, transitions at the dinucleotide CpG show the largest male predominance (11-fold). In contrast to single-base substitutions, deletions display a sex ratio of unity. Analysis of the parental age at transmission of a new mutation suggests that germ-line mutations are associated with a small increase in parental age in females but little, if any, increase in males. Although direct genomic sequencing offers a general method for defining the origin of mutation in specific families, accurate estimates of the sex ratios of different mutational classes require large sample sizes and careful correction for multiple biases of ascertainment. The biases in the present data result in an underestimate of the enhancement of mutation in males.
TL;DR: The present analyses lead to several predictions that are not consistent with a number of the frequently held assumptions in the field of molecular evolution, including belief in a constant rate of evolution, symmetric branching of phylogenetic trees, the generality of higher mutation frequency for neutral sets of nucleotides, and teleological explanations of DNA base composition.
Abstract: Using a general form of the directional mutation theory, this paper analyzes the effect of mutations in mutator genes on the G + C content of DNA, the frequency of substitution mutations, and evolutionary changes (cumulative mutations) under various degrees of selective constraints. Directional mutation theory predicts that when the mutational bias between A/T and G/C nucleotide pairs is equilibrated with the base composition of a neutral set of DNA nucleotides, the mutation frequency per gene will be much lower than the frequency immediately after the mutator mutation takes place. This prediction explains the wide variation of the DNA G + C content among unicellular organisms and possibly also the wide intragenomic heterogeneity of third codon positions for the genes of multicellular eukaryotes. The present analyses lead to several predictions that are not consistent with a number of the frequently held assumptions in the field of molecular evolution, including belief in a constant rate of evolution, symmetric branching of phylogenetic trees, the generality of higher mutation frequency for neutral sets of nucleotides, the notion that mutator mutations are generally deleterious because of their high mutation rates, and teleological explanations of DNA base composition.
TL;DR: In this article, the authors found linkage equilibrium to FRAXAC2, an Alu-associated microsatellite within the defective gene, FMR-1, which suggests that the target for tandem repeat instability may not be confined to the (CGG)nrepeat alone and raises the possibility of an FMR1 mutation mechanism involving microsatellites.
Abstract: While studying founder chromosomes in the fragile X syndrome, we have unexpectedly found linkage equilibrium to FRAXAC2, an Alu–associated microsatellite within the defective gene, FMR–1. DNA sequencing of 265 chromosomes revealed 39 alleles and a complex microsatellite of form (GT)x–C–(TA)y–(T)z. A mutation rate of 3.3% was observed but only among fragile X maternally derived meioses. Finding a second mutable locus within FMR–1 suggests that the target for tandem repeat instability may not be confined to the (CGG)nrepeat alone and raises the possibility of an FMR–1 mutation mechanism involving microsatellites.
TL;DR: This notion that it should be difficult to isolate strong, general antimutator mutations, that is, mutations that substantially lower the total spontaneous mutation rate over the entire genome without producing strongly deleterious side effects is tested by measuring mutation rates over a target comprising several kilobases in a set of phage T4 antimutators.
TL;DR: An analysis of molecular evolution in a laboratory‐generated phylogeny of the bacteriophage T7, a virus of 40 kilo‐base pairs of double‐stranded DNA, illustrates how analyses of experimental evolution in bacteriophile can be exploited to reveal relationships between the basics of molecular Evolution and abstract models of evolutionary processes.
Abstract: We present an analysis of molecular evolution in a laboratory-generated phylogeny of the bacteriophage T7, a virus of 40 kilo-base pairs of double-stranded DNA. The known biology of T7 is used in concert with observed changes in restriction sites and in DNA sequences to produce a model of restriction-site convergence and divergence in the experimental lineages. During laboratory propagation in the presence of a mutagen, the phage lineages changed an estimated 0.5%-1.5% in base pairs; most change appears to have been G → A or C → T, presumably because of the mutagen employed. Some classes of restriction-site losses can be explained adequately as simple outcomes of random processes, given the mutation rate and the bias in mutation spectrum. However, some other classes of sites appear to have undergone accelerated rates of loss, as though the losses were selectively favored. Overall, the wealth of knowledge available for T7 biology contributes only modestly to these explanations of restriction-site evolution, but rates of restriction-site gains remain poorly explained, perhaps requiring an even deeper understanding of T7 genetics than was employed here. Having measured these properties of molecular evolution, we programmed computer simulations with the parameter estimates and pseudo-replicated the empirical study, thereby providing a data base for statistical evaluation of phylogeny reconstruction methods. By these criteria, replicates of the experimental phylogeny would be correctly reconstructed over 97% of the time for the three methods tested, but the methods differed significantly both in their ability to recover the correct topology and in their ability to predict branch lengths. More generally, the study illustrates how analyses of experimental evolution in bacteriophage can be exploited to reveal relationships between the basics of molecular evolution and abstract models of evolutionary processes.
TL;DR: The steps that determine fidelity during DNA polymerization reactions are described, and several models for how DNA polymerases make DNA synthesis catalyzed by RTs are considered.
Abstract: The reported rate at which mutations are generated in retroviruses ranges from 10 −6 to 10 −4 mutations per nucleotide per cycle through a host cell (Batschelet 1976; Leider et al. 1988; Pathak and Temin 1990). Hyper-mutagenesis in spleen necrosis virus (SNV) (Pathak and Temin 1990) is one special case where the rate is even higher, 10 −2 . Such mutation rates are considerably higher than those of DNA-based microbes (Drake 1991), which range from 10 −7 to 10 −11 mutations per nucleotide per generation. Analogous to the situation in DNA-based organisms, retroviral diversity presumably results from several competing forces (Drake 1991), including the disadvantage of deleterious mutations, the advantage of rapid adaptation to a changing environment in the host, and the cost in terms of the energy required to avoid or eliminate mutations. Three different replication systems operate during the life cycle of a retrovirus. The reverse transcriptase (RT) polymerizes deoxyribonucleotides, first using viral RNA and then the newly made complementary strand DNA as a template. Cellular DNA polymerases replicate the integrated viral DNA. Finally, RNA polymerase II transcribes the proviral DNA into RNA genomes that are packaged into virions. Although it is possible for mutations to be introduced into the viral genome during any one of these replication steps, much attention has focused on the subject of this chapter, i.e., the fidelity of DNA synthesis catalyzed by RTs. We begin this review by describing the steps that determine fidelity during DNA polymerization reactions, and then we consider several models for how DNA polymerases make...