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

Kondrashov, Fyodor A.; Kondrashov, Alexey S.

doi:10.1098/rstb.2009.0286

Cited by 94 publications

(77 citation statements)

References 105 publications

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“…Two major experimental approaches have been used to study the effects of mutations on fitness (van Harten, 1998; Kondrashov & Kondrashov, 2010). First, mutation accumulation (MA) studies reduce the strength of selection on experimental populations, allowing spontaneous mutations to accumulate by drift (Halligan & Keightley, 2009; Mukai, 1964).…”

Section: Introductionmentioning

confidence: 99%

The effect of induced mutations on quantitative traits in Arabidopsis thaliana: Natural versus artificial conditions

Stearns

Fenster

2016

Ecology and Evolution

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Mutations are the ultimate source of all genetic variations. New mutations are expected to affect quantitative traits differently depending on the extent to which traits contribute to fitness and the environment in which they are tested. The dogma is that the preponderance of mutations affecting fitness will be skewed toward deleterious while their effects on nonfitness traits will be bidirectionally distributed. There are mixed views on the role of stress in modulating these effects. We quantify mutation effects by inducing mutations in Arabidopsis thaliana (Columbia accession) using the chemical ethylmethane sulfonate. We measured the effects of new mutations relative to a premutation founder for fitness components under both natural (field) and artificial (growth room) conditions. Additionally, we measured three other quantitative traits, not expected to contribute directly to fitness, under artificial conditions. We found that induced mutations were equally as likely to increase as decrease a trait when that trait was not closely related to fitness (traits that were neither survivorship nor reproduction). We also found that new mutations were more likely to decrease fitness or fitness‐related traits under more stressful field conditions than under relatively benign artificial conditions. In the benign condition, the effect of new mutations on fitness components was similar to traits not as closely related to fitness. These results highlight the importance of measuring the effects of new mutations on fitness and other traits under a range of conditions.

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Section: Introductionmentioning

confidence: 99%

The effect of induced mutations on quantitative traits in Arabidopsis thaliana: Natural versus artificial conditions

Stearns

Fenster

2016

Ecology and Evolution

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“…Historically, this has been accomplished mainly by finding single genes or groups of genes that lead to phenotypic changes that can easily be observed in populations with known descent (Drake et al 1998) and extrapolating to the level of genomes. As Kondrashov & Kondrashov (2010) point out in their contribution to this issue, the recent advances in post-genomic sequencing technology have led to breakthroughs that now allow direct determination of mutation rates in species with sequenced genomes, work which Charlesworth has stimulated by his developments of theory and to which he has contributed directly (Haag-Liautard et al 2007). Future work in this area is important because accurate estimates of mutation rates at different sites and in different species can be important for testing alternative theories.…”

Section: Mutationsmentioning

confidence: 99%

The population genetics of mutations: good, bad and indifferent

Loewe

Hill

2010

Phil. Trans. R. Soc. B

196

129

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Population genetics is fundamental to our understanding of evolution, and mutations are essential raw materials for evolution. In this introduction to more detailed papers that follow, we aim to provide an oversight of the field. We review current knowledge on mutation rates and their harmful and beneficial effects on fitness and then consider theories that predict the fate of individual mutations or the consequences of mutation accumulation for quantitative traits. Many advances in the past built on models that treat the evolution of mutations at each DNA site independently, neglecting linkage of sites on chromosomes and interactions of effects between sites (epistasis). We review work that addresses these limitations, to predict how mutations interfere with each other. An understanding of the population genetics of mutations of individual loci and of traits affected by many loci helps in addressing many fundamental and applied questions: for example, how do organisms adapt to changing environments, how did sex evolve, which DNA sequences are medically important, why do we age, which genetic processes can generate new species or drive endangered species to extinction, and how should policy on levels of potentially harmful mutagens introduced into the environment by humans be determined?

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“…Accurate estimation of the mutation rate is made difficult by the very low rate of spontaneous mutagenesis, so most estimates have been indirect, relying on DNA divergence at putatively neutral sites between species or on phenotypic screens. These approaches make several assumptions that are difficult to validate (including evolutionary divergence dates and generation intervals), limiting their precision and accuracy (reviewed by Kondrashov and Kondrashov 2010). Recently, a few studies have begun to estimate the mutation rate through direct sequencing of lines that have accumulated mutations for multiple generations or by the sequencing of parents and their offspring (Caenorhabditis elegans, Denver et al 2009;Drosophila melanogaster, Haag-Liautard et al 2007;Keightley et al 2009; Saccharomyces cerevisiae, Lynch et al 2008; Arabidopsis thaliana, Ossowski et al 2010; Homo sapiens, Xue et al 2009;Roach et al 2010;Conrad et al 2011;Kong et al 2012).…”

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confidence: 99%

Estimate of the Spontaneous Mutation Rate in Chlamydomonas reinhardtii

Morgan²,

et al. 2012

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The nature of spontaneous mutations, including their rate, distribution across the genome, and fitness consequences, is of central importance to biology. However, the low rate of mutation has made it difficult to study spontaneous mutagenesis, and few studies have directly addressed these questions. Here, we present a direct estimate of the mutation rate and a description of the properties of new spontaneous mutations in the unicellular green alga Chlamydomonas reinhardtii. We conducted a mutation accumulation experiment for 350 generations followed by whole-genome resequencing of two replicate lines. Our analysis identified a total of 14 mutations, including 5 short indels and 9 single base mutations, and no evidence of larger structural mutations. From this, we estimate a total mutation rate of 3.23 · 10 210 /site/generation (95% C.I. 1.82 · 10 210 to 5.23 · 10 210 ) and a single base mutation rate of 2.08 · 10 210 /site/generation (95% C.I., 1.09 · 10 210 to 3.74 · 10 210 ). We observed no mutations from A/T / G/C, suggesting a strong mutational bias toward A/T, although paradoxically, the GC content of the C. reinhardtii genome is very high. Our estimate is only the second direct estimate of the mutation rate from plants and among the lowest spontaneous base-substitution rates known in eukaryotes. N EW mutations are the ultimate source of the genetic variation necessary for adaptation via natural selection. Moreover, the mutation rate has profound consequences for a myriad of disciplines, including conservation, genetics, medicine, and evolution. The rate of new mutations influences both the speed at which populations respond to natural selection and the rate at which fitness may decline due to inbreeding. The rate, strength, and sign of fitness effects of new mutations are critical parameters of models of the evolution and maintenance of sexual reproduction. Currently, however, characterization of the rates, causes, and effects of different kinds of mutations is lacking.Although mutation is fundamentally important for adaptive change, the vast majority of mutations influencing fitness are generally believed to be deleterious (Keightley and Lynch 2003; but see Shaw et al. 2002;Rutter et al. 2010). For this reason, most theory, especially in recombining populations, predicts that selection will drive mutation to lower and lower rates (Kimura 1967;Kondrashov 1995;Dawson 1999;Lynch 2008). Even when a mutator allele increasing the mutation rate arises and produces a beneficial mutation, recombination will tend to disassociate the mutator from the beneficial mutation, eliminating any benefit it may gain from hitchhiking (for example, Raynes et al. 2011). Although selection is expected to drive the mutation rate toward zero, the mutation rate remains detectably above zero.Relatively few studies have estimated the spontaneous mutation rate directly through the sequencing of a large fraction of the genome (see below). Accurate estimation of the mutation rate is made difficult by the very low rate of spontan...

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

Cited by 94 publications

References 105 publications

The effect of induced mutations on quantitative traits in Arabidopsis thaliana: Natural versus artificial conditions

The effect of induced mutations on quantitative traits in Arabidopsis thaliana: Natural versus artificial conditions

The population genetics of mutations: good, bad and indifferent

Estimate of the Spontaneous Mutation Rate in Chlamydomonas reinhardtii

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