The Genetic Structure of Natural Populations of Drosophila Melanogaster. I. Spontaneous Mutation Rate of Polygenes Controlling Viability

Mukai, Terumi

doi:10.1093/genetics/50.1.1

Cited by 419 publications

(54 citation statements)

References 13 publications

(11 reference statements)

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“…The tests of departure from neutrality studied here offer (in principle) the possibility of determining whether observed instances of reduced genetic diversity could be explained by background selection. But significant departures of allele frequency spectra from expectations under neutrality (as assessed by the values of TAJIMA'S or Fu and LI'S statistics, or by Watterson's test) are unlikely to be found under background selection with the "standard" sh value of 0.02 that corresponds to the estimated harmonic mean selection coefficient against a heterozygous detrimental mutation in Drosophila (MUKAI 1964;MUKAI et al 1972;CROW and SIMMONS 1983). This remains true even when the true population size is small, so that the x and 8 values (relative to neutral expectation) for the population are expected to differ widely.…”

Section: Discussionmentioning

confidence: 99%

The pattern of neutral molecular variation under the background selection model.

Charlesworth¹,

Charlesworth²,

Morgan³

1995

Genetics

371

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Stochastic simulations of the infinite sites model were used to study the behavior of genetic diversity at a neutral locus in a genomic region without recombination, but subject to selection against deleterious alleles maintained by recurrent mutation (background selection). In large populations, the effect of background selection on the number of segregating sites approaches the effect on nucleotide site diversity, i.e., the reduction in genetic variability caused by background selection resembles that caused by a simple reduction in effective population size. We examined, by coalescence-based methods, the power of several tests for the departure from neutral expectation of the frequency spectra of alleles in samples from randomly mating populations (Tajima's, Fu and Li's, and Watterson's tests). All of the tests have low power unless the selection against mutant alleles is extremely weak. In Drosophila, significant Tajima's tests are usually not obtained with empirical data sets from loci in genomic regions with restricted recombination frequencies and that exhibit low genetic diversity. This is consistent with the operation of background selection as opposed to selective sweeps. It remains to be decided whether background selection is sufficient to explain the observed extent of reduction in diversity in regions of restricted recombination.

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Section: Discussionmentioning

confidence: 99%

The pattern of neutral molecular variation under the background selection model.

Charlesworth¹,

Charlesworth²,

Morgan³

1995

Genetics

371

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“…Mutations have been the subject of quantitative research for quite some time (Danforth 1923;Muller 1927;Haldane 1935;Timofeeff-Ressovsky 1935;Mukai 1964;Mukai et al 1972;Crow & Abrahamson 1997) and there have been many attempts at estimating the rates of spontaneous mutations (for a review, see Drake 1993;Drake et al 1998;Lynch et al 1999Baer et al 2007). The efforts of the past century have produced a fragmented picture.…”

Section: Introductionmentioning

confidence: 99%

Measurements of spontaneous rates of mutations in the recent past and the near future

Kondrashov

2010

Phil. Trans. R. Soc. B

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The rate of spontaneous mutation in natural populations is a fundamental parameter for many evolutionary phenomena. Because the rate of mutation is generally low, most of what is currently known about mutation has been obtained through indirect, complex and imprecise methodological approaches. However, in the past few years genome-wide sequencing of closely related individuals has made it possible to estimate the rates of mutation directly at the level of the DNA, avoiding most of the problems associated with using indirect methods. Here, we review the methods used in the past with an emphasis on next generation sequencing, which may soon make the accurate measurement of spontaneous mutation rates a matter of routine.

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“…If a model of equal mutant effects is assumed, genotypic values have the same distribution as that of numbers of mutations, namely Poisson, and the change of mean and variance provide information for inference of mutation rate and mean mutant effect (MUKAI 1964).…”

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confidence: 99%

The distribution of mutation effects on viability in Drosophila melanogaster.

Keightley¹

1994

Genetics

223

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Parameters of continuous distributions of effects and rates of spontaneous mutation for relative viability in Drosophila are estimated by maximum likelihood from data of two published experiments on accumulation of mutations on protected second chromosomes. A model of equal mutant effects gives a poor fit to the data of the two experiments; higher likelihoods are obtained with leptokurtic distributions or for models in which there is more than one class of mutation effect. Minimum estimates of mutation rates (events per generation) at polygenes affecting viability on chromosome 2 are 0.14 and 0.068, but estimates are strongly confounded with other parameters in the model. Separate information on rates of molecular divergence between Drosophila species and from rates of movement of transposable elements is used to infer the overall genomic mutation rate in Drosophila, and the viability data are analyzed with mutation rate as a known parameter. If, for example, a mutation rate for chromosome 2 of 0.4 is assumed, maximum likelihood estimates of mean mutant effect on relative viability are 0.4% and 1%, but the majority of mutations have very much smaller effects than these values as distributions are highly leptokurtic. The methodology is applied to estimate viability effects of single P element insertional mutations. The mean effect per insertion is found to be higher, and their distribution is found to be less leptokurtic than for spontaneous mutations. The equilibrium genetic variance of viability predicted by a mutation-selection balance model with parameters estimated from the mutation accumulation experiments is similar to laboratory estimates of genetic variance of viability from natural populations of Drosophila.

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The Genetic Structure of Natural Populations of Drosophila Melanogaster. I. Spontaneous Mutation Rate of Polygenes Controlling Viability

Cited by 419 publications

References 13 publications

The pattern of neutral molecular variation under the background selection model.

The pattern of neutral molecular variation under the background selection model.

Measurements of spontaneous rates of mutations in the recent past and the near future

The distribution of mutation effects on viability in Drosophila melanogaster.

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