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Results for “deleterious mutation”

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PubMed2003

Mutational analysis of BARD1 in familial breast cancer patients in Japan.

Since BRCA1,which is a breast cancer susceptibility gene, form heterodimers with BARD1, it is speculated that BARD1 mutations might affect the function of BRCA1, contributing to breast carcinogenesis. Thus, in the present study, we have conducted mutational analysis of BARD1 in familial breast cancer patients (n=60) who were tested negative for both BRCA1 and BRCA2 germline mutations. We have been unable to show any clearly deleterious mutations but identified four missence mutations (Ser/Cys 241, Arg/Ser 378, Asn/Ser 470, Val/Met 507), one silent mutation (His/His 506), and one frameshift (in-frame) mutation (1139del21bp). Of these six mutations, one (Asn/Ser 470) was considered as a putative germline mutation since such a mutation was not observed in any of the healthy controls (n=152) but the other five mutations were considered as common genetic polymorphisms since they were frequently observed in the healthy controls. These genetic polymorphisms were further analyzed in their association with breast cancer risk by a case-control study using the population-based breast cancers (n=143) and healthy controls (n=155), which showed that carriers of the variant allele Met at codon 507 are significantly associated with the increased risk of breast cancer (adjusted odds ratio=2.05, 95% confidential interval=1.01-4.16) in postmenopausal women and that the other genetic polymorphisms are not associated with breast cancer risk. These results suggest that BARD1 mutations are responsible for, if any, a very small number of familial breast cancers. Genetic polymorphism of BARD1 (Val/Met 507) could be useful in the selection of postmenopausal women at a high risk for developing breast cancer.

Breast Neoplasms↗

PubMed2001

Is the population size of a species relevant to its evolution?

This paper examines aspects of genetic draft, the stochastic force induced by substitutions at one locus on the dynamics of a closely linked locus. Of particular interest is the role of population size on genetic draft. Remarkably, the rate of substitution of weakly selected advantageous mutations decreases with increasing population size, whereas that for deleterious mutations increases with population size. This dependency on population size is the opposite of that for genetic drift. Moreover, these rates are only weakly dependent on population size, again contrary to the strong dependency of drift-based dynamics. Four models of the strongly selected loci responsible for genetic draft are examined. Three of these exhibit a very weak dependency on population size, which implies that their induced effects will also be weakly dependent on population size. Together, these results suggest that population size and binomial sampling may not be relevant to a species' evolution. If this is the case, then a number of evolutionary conundrums are resolved.

Alleles↗

PubMed2004

The speed of adaptation in large asexual populations.

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

Adaptation, Physiological↗

PubMedDate not supplied

The mutational meltdown in asexual populations.

Loss of fitness due to the accumulation of deleterious mutations appears to be inevitable in small, obligately asexual populations, as these are incapable of reconstituting highly fit genotypes by recombination or back mutation. The cumulative buildup of such mutations is expected to lead to an eventual reduction in population size, and this facilitates the chance accumulation of future mutations. This synergistic interaction between population size reduction and mutation accumulation leads to an extinction process known as the mutational meltdown, and provides a powerful explanation for the rarity of obligate asexuality. We give an overview of the theory of the mutational meltdown, showing how the process depends on the demographic properties of a population, the properties of mutations, and the relationship between fitness and number of mutations incurred.

Biological Evolution↗

PubMed2001

Soluble model for the accumulation of mutations in asexual populations.

Finite asexual populations can accumulate an increasing number of deleterious mutations by a process known as Muller's ratchet, which consists of successive losses of the fittest or least-loaded classes of individuals in the population. We present here a simplified theoretical framework to describe the serial bottleneck passages setup used in experiments to demonstrate the decrease of the population mean fitness due to the operation of ratchet. In particular, we calculate the expected time between consecutive clicks of the ratchet and derive expressions relating the moments of the mean fitness distribution to the mutation and selection parameters.

Models, Genetic↗

PubMed2003

Dominance of mutations affecting viability in Drosophila melanogaster.

There have been several attempts to estimate the average dominance (ratio of heterozygous to homozygous effects) of spontaneous deleterious mutations in Drosophila melanogaster, but these have given inconsistent results. We investigated whether transposable element (TE) insertions have higher average dominance for egg-to-adult viability than do point mutations, a possibility suggested by the types of fitness-depressing effects that TEs are believed to have. If so, then variation in dominance estimates among strains and crosses would be expected as a consequence of variation in TE activity. As a first test, we estimated the average dominance of all mutations and of copia insertions in a set of lines that had accumulated spontaneous mutations for 33 generations. A traditional regression method gave a dominance estimate for all mutations of 0.17, whereas average dominance of copia insertions was 0.51; the difference between these two estimates approached significance (P = 0.08). As a second test, we reanalyzed Ohnishi 1974 data on dominance of spontaneous and EMS-induced mutations. Because a considerable fraction of spontaneous mutations are caused by TE insertions, whereas EMS induces mainly point mutations, we predicted that average dominance would decline with increasing EMS concentration. This pattern was observed, but again fell short of formal significance (P = 0.07). Taken together, however, the two results give modest support for the hypothesis that TE insertions have greater average dominance in their viability effects than do point mutations, possibly as a result of deleterious effects of expression of TE-encoded genes.

Animals↗

PubMed1998

Should we expect substitution rate to depend on population size?

The rate of nucleotide substitution is generally believed to be a decreasing function of effective population size, at least for nonsynonymous substitutions. This view was originally based on consideration of slightly deleterious mutations with a fixed distribution of selection coefficients. A realistic model must include the occurrence and fixation of some advantageous mutations that compensate for the loss of fitness due to deleterious substitutions. Some such models, such as so-called "fixed" models, also predict a population size effect on substitution rate. An alternative model, presented here, predicts the near absence of a population size effect on substitution rate. This model is based on concave log-fitness functions and a fixed distribution of mutational effects on the selectively important trait. Simulations of an instance of the model confirm the approximate insensitivity of the substitution rate to population size. Although much experimental evidence has been claimed to support the existence of a population size effect, the body of evidence as a whole is equivocal, and much of the evidence that is supposed to demonstrate such an effect would also suggest that it is very small. Perhaps the proposed model applies well to some genes and not so well to others, and genes therefore vary with regard to the population size effect.

Amino Acid Substitution↗

PubMed1998

Requisite mutational load, pathway epistasis and deterministic mutation accumulation in sexual versus asexual populations.

A measure of the equilibrium load of deleterious mutations is developed that explicitly incorporates the level of genome-wide linkage disequilibrium. This measure, called the requisite mutational load, is based on the minimal net reproductive rate of the least mutated class necessary to prevent the deterministic mutation accumulation. If this minimal net reproductive rate is larger than ecological or physiological constraints allow, then: a) the population is driven to extinction via deterministic mutation accumulation, or b) a mutational Red-Queen ensues with adaptation counterbalancing mutation accumulation. Two population parameters determine the requisite mutational load: a) the equilibrium strength of selection, measured as a selection gradient, and b) the equilibrium opportunity for selection, measured as the variance in number of mutations per genome. The opportunity for selection is decomposed into the accumulation of mutations (average number per genome) and the level of genome-wide linkage disequilibrium. Recombination can substantially reduce the requisite mutational load, compared to clonal reproduction, when there is buffering and/or reinforcing epistasis and also when there is positive assortative mating for fitness. Recombination is advantageous because it reduces the negative (variance reducing) linkage disequilibrium induced by beneficial epistasis. The functional form of the expression for requisite mutational load illustrates why epistasis within pathways, i.e., among closely interacting genes, is a powerful alternative to genome-wide truncation selection, as a means of reducing mutational load.

Animals↗

PubMed1984

Males and the advantage of sex.

Most sexual populations are at a two-fold disadvantage to parthenogenetic populations. This is because males are produced in equal numbers to females and males contribute virtually no food supplies to the zygote. Females therefore "waste their energy" in the production of sons. Parthenogenetic females produce only daughters and therefore have a two-fold advantage. It is argued that female choice (of males) and male: male competition can reduce mutational loads and this may compensate for the two-fold disadvantage of males. The Haldane mutation load principle indicates a load of 2mu, where mu is the mutation rate per gamete. Female choice and male: male competition are capable of reducing this substantially. The effect is greatest with mildly deleterious mutations and is therefore dependent on the fitness of the mutations. This is in contrast to the Haldane principle load which is determined by the mutation rate only. As most mutations appear to be mildly deleterious the load in many sexual populations may be substantially below that indicated by the Haldane principle.

Animals↗

PubMed2005

The roles of positive and negative selection in the molecular evolution of insect endosymbionts.

The evolutionary rate acceleration observed in most endosymbiotic bacteria may be explained by higher mutation rates, changes in selective pressure, and increased fixation of deleterious mutations by genetic drift. Here, we explore the forces influencing molecular evolution in Blochmannia, an obligate endosymbiont of Camponotus and related ant genera. Our goals were to compare rates of sequence evolution in Blochmannia with related bacteria, to explore variation in the strength and efficacy of negative (purifying) selection, and to evaluate the effect of positive selection. For six Blochmannia pairs, plus Buchnera and related enterobacteria, estimates of sequence divergence at four genes confirm faster rates of synonymous evolution in the ant mutualist. This conclusion is based on higher dS between Blochmannia lineages despite their more recent divergence. Likewise, generally higher dN in Blochmannia indicates faster rates of nonsynonymous substitution in this group. One exception is the groEL gene, for which lower dN and dN/dS compared to Buchnera indicate exceptionally strong negative selection in Blochmannia. In addition, we explored evidence for positive selection in Blochmannia using both site-and lineage-based maximum likelihood models. These approaches confirmed heterogeneity of dN/dS among codon sites and revealed significant variation in dN/dS across Blochmannia lineages for three genes. Lineage variation affected genes independently, with no evidence of parallel changes in dN/dS across genes along a given branch. Our data also reveal instances of dN/dS greater than one; however, we do not interpret these large dN/dS ratios as evidence for positive selection. In sum, while drift may contribute to an overall rate acceleration at nonsynonymous sites in Blochmannia, variable selective pressures best explain the apparent gene-specific changes in dN/dS across lineages of this ant mutualist. In the course of this study, we reanalyzed variation at Buchnera groEL and found no evidence of positive selection that was previously reported.

Animals↗

PubMed2001

Response to Kondrashov.

The 'mutational deterministic' hypothesis proposes that a high genomic rate of deleterious mutation (U) might maintain sexual reproduction. Our recent work casts doubt on this, as we estimate a low U for sexually reproducing species with short generation times. Following criticism by Kondrashov, here we defend our methods for estimating U and challenge the mutational deterministic hypothesis.

Animals↗

PubMed2006

Genetic load in subdivided populations: interactions between the migration rate, the size and the number of subpopulations.

We assess the relative importance of migration rate, size and number of subpopulations on the genetic load of subdivided populations. Using diffusion approximations, we show that in most cases subdivision has detrimental effects on fitness. Moreover, our results suggest that fitness increases with subpopulation size, so that for the same total population size, genetic load is relatively lower when there are a small number of large subpopulations. Using elasticity analysis, we show that the size of the subpopulations appears to be the parameter that most strongly determines genetic load. interconnecting subpopulations via migration would also be of importance for population fitness when subpopulations are small and gene flow is low. Interestingly, the number of subpopulations has minor influence on genetic load except for the case of both very slightly deleterious mutations and small subpopulations. Elasticities decrease as the magnitude of deleterious effects increases. In other words, population structure does not matter for very deleterious alleles, but strongly affects fitness for slightly deleterious alleles.

Alleles↗

PubMed2000

Shattered: Medawar's test tubes and their enduring legacy of chaos.

Medawar's 1952 paper 'An Unsolved Problem of Biology' underlies most subsequent theoretical work regarding the evolution of aging; it concludes that aging is accidental and could not have evolved; this prevents reconciling the growing body of evidence suggesting the existence of multiple, evolved, aging systems. The paper features a well-known thought experiment using test tubes to show why aging could not evolve. Medawar assumes that constant, random, breakage sufficiently represents lethal forces of nature; however, famine, drought, predation, disease, and accidents each uniquely affect populations. Predation is the only evolving force that continually invents new ways to kill members of the prey populations; thus all prey defenses to predation will eventually be defeated. Defenses to non-evolving or non-obligate lethal forces, however, should quickly evolve. Thus unevolving, identical test tubes cannot adequately represent biological populations. The example also ignores population booms and busts which often occur in nature. By ignoring these issues, Medawar examines only one population age distribution skewed towards younger individuals in predator-dominated environments while ignoring predator-free populations skewed towards older individuals after population crashes. Further, Medawar's test tubes lack meaningful competition for finite resources, and ignore declining fertility which occurs in all aging species. Medawar concludes that older individuals are too few in number to influence the population's gene pool for or against aging. This conclusion is found to be incorrect when variations in the age of reproductive senescence are introduced into a predator-free population.A new thought experiment with competing strains of algae corrects for these issues and shows that aging evolved and is retained so that groups retain enough genetic variability to allow for rapid evolution of a defense to novel predation. The example shows reasons why the rate of aging is directly linked to the reproductive rate, litter size, metabolic rate, reproductive senescence, and fixed body size. It also suggests that in the absence of predation, immortality would quickly evolve if not for the evolution of highly-conserved aging systems. Prior analysis of aging evolution is incorrect due to theorists' rejection of the idea of group selection. It is believed to be 'impossible' to select for mutations that are bad for the individual but good for the group. However, mutations that are neutral to young individuals which are only deleterious if expressed at older ages can accumulate in early-mortality, predator-dominated environments. Removing the predator allows deleterious mutation expression. Positive group selection then occurs amongst traits that are negative to the individual. Further, group selection is a universal force that occurs between local, non-breeding groups and not, as theorists propose, between distant groups of potentially interbreeding species. Local survivors migrate to replace extinct, related species. The antagonistic pleiotropy theory, which was created to salvage the idea of accidental aging, is examined and shown to be untenable. The hypothetical antagonistic pleiotropy genes that are beneficial to young while detrimental to old individuals, predicted to exist in the 1950s, are unlikely to exist, have not, and likely will not be found in sufficient quantity to participate in the aging process.

Aging↗

PubMed2005

Structures of p53 cancer mutants and mechanism of rescue by second-site suppressor mutations.

We have solved the crystal structures of three oncogenic mutants of the core domain of the human tumor suppressor p53. The mutations were introduced into a stabilized variant. The cancer hot spot mutation R273H simply removes an arginine involved in DNA binding without causing structural distortions in neighboring residues. In contrast, the "structural" oncogenic mutations H168R and R249S induce substantial structural perturbation around the mutation site in the L2 and L3 loops, respectively. H168R is a specific intragenic suppressor mutation for R249S. When both cancer mutations are combined in the same molecule, Arg(168) mimics the role of Arg(249) in wild type, and the wild type conformation is largely restored in both loops. Our structural and biophysical data provide compelling evidence for the mechanism of rescue of mutant p53 by intragenic suppressor mutations and reveal features by which proteins can adapt to deleterious mutations.

Arginine↗

PubMed2001

Estimates of the rate and distribution of fitness effects of spontaneous mutation in Saccharomyces cerevisiae.

The per-genome, per-generation rate of spontaneous mutation affecting fitness (U) and the mean fitness cost per mutation (s) are important parameters in evolutionary genetics, but have been estimated for few species. We estimated U and sh (the heterozygous effect of mutations) for two diploid yeast strains differing only in the DNA mismatch-repair deficiency used to elevate the mutation rate in one (mutator) strain. Mutations were allowed to accumulate in 50 replicate lines of each strain, during 36 transfers of randomly chosen single colonies (approximately 600 generations). Among wild-type lines, fitnesses were bimodal, with one mode showing no change in mean fitness. The other mode showed a mean 29.6% fitness decline and the petite phenotype, usually caused by partial deletion of the mitochondrial genome. Excluding petites, maximum-likelihood estimates adjusted for the effect of selection were U = 9.5 x 10(-5) and sh = 0.217 for the wild type. Among the mutator lines, the best fit was obtained with 0.005 < or = U < or = 0.94 and 0.049 > or = sh > or = 0.0003. Like other recently tested model organisms, wild-type yeast have low mutation rates, with high mean fitness costs per mutation. Inactivation of mismatch repair increases the frequency of slightly deleterious mutations by approximately two orders of magnitude.

Base Pair Mismatch↗

PubMed2001

Transition between stochastic evolution and deterministic evolution in the presence of selection: general theory and application to virology.

We present here a self-contained analytic review of the role of stochastic factors acting on a virus population. We develop a simple one-locus, two-allele model of a haploid population of constant size including the factors of random drift, purifying selection, and random mutation. We consider different virological experiments: accumulation and reversion of deleterious mutations, competition between mutant and wild-type viruses, gene fixation, mutation frequencies at the steady state, divergence of two populations split from one population, and genetic turnover within a single population. In the first part of the review, we present all principal results in qualitative terms and illustrate them with examples obtained by computer simulation. In the second part, we derive the results formally from a diffusion equation of the Wright-Fisher type and boundary conditions, all derived from the first principles for the virus population model. We show that the leading factors and observable behavior of evolution differ significantly in three broad intervals of population size, N. The "neutral limit" is reached when N is smaller than the inverse selection coefficient. When N is larger than the inverse mutation rate per base, selection dominates and evolution is "almost" deterministic. If the selection coefficient is much larger than the mutation rate, there exists a broad interval of population sizes, in which weakly diverse populations are almost neutral while highly diverse populations are controlled by selection pressure. We discuss in detail the application of our results to human immunodeficiency virus population in vivo, sampling effects, and limitations of the model.

Biological Evolution↗

PubMed1999

Hereditary susceptibility to breast cancer: significance of age of onset in family history and contribution of BRCA1 and BRCA2.

OBJECTIVE: To correlate mutations in BRCA1 and BRCA2 with family history of breast cancer in a first-degree relative for women diagnosed with breast cancer before age 45 who do not have a personal or family history of ovarian cancer. METHODS: Family history for women with breast cancer diagnosed before age 45 was provided by ordering physicians via a test requisition form designed for this purpose. Gene analysis was performed by dye primer sequencing for the entire coding regions of BRCA1 and BRCA2. Because a personal and family history of ovarian cancer are known to be significantly associated with mutations, women with either were excluded from analysis. RESULTS: Overall, deleterious mutations in BRCA1 or BRCA2 were identified in 85 of 440 women (19%) with breast cancer under 45. Mutations were identified in 73 of 276 women (26%) with a first degree family history of breast cancer compared to 12 of 164 without (7%) (P < .0001). When results were analyzed by the age of diagnosis in first degree relatives, mutations were identified in 56 of 185 women (30%) with at least one first degree relative with breast cancer diagnosed before age 50 compared with 17 of 91 women (19%), where the first degree family history of breast cancer was at or over age 50 (P = .042). CONCLUSION: Among women with breast cancer diagnosed before age 45, a first-degree relative diagnosed with the disease under age 50 is an indicator of a mutation in BRCA1 or BRCA2 even in the absence of a family history of ovarian cancer. Therefore, women diagnosed with early-onset breast cancer should be asked about the age of onset in any first-degree relative diagnosed with the disease, as well as about any family history of ovarian cancer. Mutations in BRCA2 account for a substantial proportion of hereditary breast cancer. Therefore, studies that are limited to BRCA1 or that do not analyze by age of onset of breast cancer in relatives may underestimate the contribution of mutations in BRCA1 and BRCA2 to women with early onset breast cancer.

Adult↗

PubMed1998

Hereditary Factors in Gynecologic Cancer.

Cancer predisposition in some families is known to be the result of germ-line mutations. The most noteworthy hereditary gynecologic cancer syndromes include hereditary breast-ovarian cancer (HBOC) syndrome, wherein BRCA1 and BRCA2 germ-line mutations have been identified, and hereditary nonpolyposis colorectal cancer (HNPCC) of the Lynch syndrome II variant, wherein hMSH2, hMLH1, hPMS2, hMSH3, and hMSH6 germ-line mutations have been identified. DNA testing for specific cancer-associated germ-line mutations is now available for HBOC and HNPCC syndrome family members who are in the direct line of inheritance. Genetic counseling is mandatory prior to DNA testing and at the time of disclosure of findings. A patient found to be negative for the family's particular cancer-associated germ-line mutation can revert to general population screening recommendations. When a deleterious mutation is identified, the physician is able to predict a patient's lifetime susceptibility to breast and ovarian carcinomas in the HBOC syndrome or the cancers which characterize the Lynch syndrome II variant of HNPCC, particularly carcinomas of the colon, endometrium, and ovary. Management strategies can be offered which are designed to take advantage of the natural history of that distinct hereditary cancer syndrome. We discuss the unfolding developments concerning familial and heritable susceptibilities, molecular genetics, and possible carcinogenic co-factors of the three most common gynecologic cancers: carcinomas of the uterine cervix, endometrium, and ovary. We offer rationales for management based on current epidemiologic and clinical data and emerging technologies.

Journal Article↗