Clusters of identical new mutation in the evolutionary landscape

Rc, Woodruff; Huai, Haiying; Jn, Thompson

doi:10.1007/bf00121363

Cited by 40 publications

(37 citation statements)

References 61 publications

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“…Thus the starting frequency of a new allele should be c /2 N on average instead of 1/2 N for a population with N individuals, i.e., p = c /2 N [15] . This affects the average survival time of a mutant allele, and formula (3) should be modifi ed as…”

Section: Resultsmentioning

confidence: 99%

“…Recent studies have shown the existence of clusters in many organisms, such as Drosophila , mice and humans [13][14][15][16][17][18][19][20][21][22][23] . In humans, premeiotic clusters of mutation are common and have been reported for base-pair changes, deletions, insertions, duplications, chromosome rearrangements, trinucleotide repeats and aneuploidy [15,20,[22][23][24] . In a literature survey of 22 genetic syndromes in humans, a new mutation arose from a germinal mosaic parent in eleven percent of the cases (266 families out of 2,459 total families; details can be obtained from the authors).…”

Section: Introductionmentioning

confidence: 99%

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The Influence of Premeiotic Clusters of Mutation on Indirect Estimations of Mutation Rate

Gong¹,

Gu²,

Woodruff³

2005

Hum Hered

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Based on the hypothesis that rare alleles are in mutation and random loss equilibrium, mutation rate can be indirectly estimated by measuring the number of rare variants and the average existing time of a mutant allele. This method can be applied to estimate the mutation rate in humans. However, this estimation of mutation rate is affected by the presence of premeiotic clusters of mutation. Mutation clusters change both the number of initial mutants and the average existing time of a mutant allele. As a result, the formula indirectly estimating mutation rate should be modified. The influence of premeiotic clusters is more obvious when the population size is small or the average cluster size is big. For example, if the population size is 3,000 and average cluster size is two, instead of one, the mutation rate is increased by about 9.4%.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The Influence of Premeiotic Clusters of Mutation on Indirect Estimations of Mutation Rate

Gong¹,

Gu²,

Woodruff³

2005

Hum Hered

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“…The mutation screening experiment employs a three-generation assay to screen autosomal recessive lethal or nearly lethal mutations in about 1,200 genes in D. melanogaster (18), which takes advantage of the balancer chromosomes that were pioneered by H. J. Muller for the purpose of maintaining newly isolated mutations, including recessive lethals, without selection (21,22). Balancers for each of the major chromosomes of D. melanogaster contain multiple inversions and one or more dominant visible mutations.…”

Section: Methodsmentioning

confidence: 99%

“…A similar mating scheme as described above was used successfully in earlier assays for the occurrence of mutation clusters in several laboratories (17,18,(25)(26)(27). It was estimated that lethal or nearly lethal mutations identified by the assay span over about 1,200 genes.…”

Section: Methodsmentioning

confidence: 99%

Highly variable recessive lethal or nearly lethal mutation rates during germ-line development of male Drosophila melanogaster

Gao

Pan

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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Each cell of higher organism adults is derived from a fertilized egg through a series of divisions, during which mutations can occur. Both the rate and timing of mutations can have profound impacts on both the individual and the population, because mutations that occur at early cell divisions will affect more tissues and are more likely to be transferred to the next generation. Using large-scale multigeneration screening experiments for recessive lethal or nearly lethal mutations of Drosophila melanogaster and recently developed statistical analysis, we show for male D. melanogaster that (i) mutation rates (for recessive lethal or nearly lethal) are highly variable during germ cell development; (ii) first cell cleavage has the highest mutation rate, which drops substantially in the second cleavage or the next few cleavages; (iii) the intermediate stages, after a few cleavages to right before spermatogenesis, have at least an order of magnitude smaller mutation rate; and (iv) spermatogenesis also harbors a fairly high mutation rate. Because germ-line lineage shares some (early) cell divisions with somatic cell lineage, the first conclusion is readily extended to a somatic cell lineage. It is conceivable that the first conclusion is true for most (if not all) higher organisms, whereas the other three conclusions are widely applicable, although the extent may differ from species to species. Therefore, conclusions or analyses that are based on equal mutation rates during development should be taken with caution. Furthermore, the statistical approach developed can be adopted for studying other organisms, including the human germ-line or somatic mutational patterns.within-host coalescent | mutation cluster | likelihood

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“…Alternatively, such information can be obtained from traditional experiments, particularly for some model organisms. For Drosophila, multigeneration mutation screening has been well developed (Muller 1928;Woodruff et al 1984Woodruff et al , 1996Ashburner 1989;Greenspan 1997) and one such system was used by Gao et al (2011) for the purpose of identifying recessive lethal or nearly lethal mutations. More experimental detail can be found in Gao et al (2011) and for the main purpose of this article, it should suffice to outline the structure of information and the type of mutation being examined.…”

Section: Definitions and Notationsmentioning

confidence: 99%

Statistical Methods for Analyzing Drosophila Germline Mutation Rates

2013

Genetics

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Most studies of mutation rates implicitly assume that they remain constant throughout development of the germline. However, researchers recently used a novel statistical framework to reveal that mutation rates differ dramatically during sperm development in Drosophila melanogaster. Here a general framework is described for the inference of germline mutation patterns, generated from either mutation screening experiments or DNA sequence polymorphism data, that enables analysis of more than two mutations per family. The inference is made more rigorous and flexible by providing a better approximation of the probabilities of patterns of mutations and an improved coalescent algorithm within a single host with realistic assumptions. The properties of the inference framework, both the estimation and the hypothesis testing, were investigated by simulation. The refined inference framework is shown to provide (1) nearly unbiased maximum-likelihood estimates of mutation rates and (2) robust hypothesis testing using the standard asymptotic distribution of the likelihood-ratio tests. It is readily applicable to data sets in which multiple mutations in the same family are common.

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Clusters of identical new mutation in the evolutionary landscape

Cited by 40 publications

References 61 publications

The Influence of Premeiotic Clusters of Mutation on Indirect Estimations of Mutation Rate

The Influence of Premeiotic Clusters of Mutation on Indirect Estimations of Mutation Rate

Highly variable recessive lethal or nearly lethal mutation rates during germ-line development of male Drosophila melanogaster

Statistical Methods for Analyzing Drosophila Germline Mutation Rates

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