scholarly journals Old Trade, New Tricks: Insights into the Spontaneous Mutation Process from the Partnering of Classical Mutation Accumulation Experiments with High-Throughput Genomic Approaches

2018 ◽  
Vol 11 (1) ◽  
pp. 136-165 ◽  
Author(s):  
Vaishali Katju ◽  
Ulfar Bergthorsson
Keyword(s):  
High Throughput ◽  
Spontaneous Mutation ◽  
Mutation Accumulation ◽  
Mutation Process ◽  
Classical Mutation

scholarly journals Nature of Deleterious Mutation Load in Drosophila

Genetics ◽  
1996 ◽  
Vol 144 (4) ◽  
pp. 1993-1999 ◽  
Author(s):  
Peter D Keightley
Keyword(s):  
Deleterious Mutation ◽  
Spontaneous Mutation ◽  
Mutation Accumulation ◽  
Mutation Rates ◽  
Mutation Load ◽  
Spontaneous Mutation Rate ◽  
A Minor ◽  
Chromosome I ◽  
Balancer Chromosomes ◽  
Balancer Chromosome

Much population genetics and evolution theory depends on knowledge of genomic mutation rates and distributions of mutation effects for fitness, but most information comes from a few mutation accumulation experiments in Drosophila in which replicated chromosomes are sheltered from natural selection by a balancer chromosome. I show here that data from these experiments imply the existence of a large class of minor viability mutations with approximately equivalent effects. However, analysis of the distribution of viabilities of chromosomes exposed to EMS mutagenesis reveals a qualitatively different distribution of effects lacking such a minor effects class. A possible explanation for this difference is that transposable element insertions, a common class of spontaneous mutation event in Drosophila, frequently generate minor viability effects. This explanation would imply that current estimates of deleterious mutation rates are not generally applicable in evolutionary models, as transposition rates vary widely. Alternatively, much of the apparent decline in viability under spontaneous mutation accumulation could have been nonmutational, perhaps due to selective improvement of balancer chromosomes. This explanation accords well with the data and implies a spontaneous mutation rate for viability two orders of magnitude lower than previously assumed, with most mutation load attributable to major effects.

scholarly journals First Estimation of the Spontaneous Mutation Rate in Diatoms

2019 ◽  
Vol 11 (7) ◽  
pp. 1829-1837 ◽  
Author(s):  
Marc Krasovec ◽  
Sophie Sanchez-Brosseau ◽  
Gwenael Piganeau
Keyword(s):  
Mutation Rate ◽  
Spontaneous Mutation ◽  
Mutation Accumulation ◽  
Mutation Rates ◽  
Model Organisms ◽  
Base Substitution ◽  
Unicellular Eukaryote ◽  
Fundamental Parameter ◽  
Secondary Endosymbiosis ◽  
Spontaneous Mutation Rate

Abstract Mutations are the origin of genetic diversity, and the mutation rate is a fundamental parameter to understand all aspects of molecular evolution. The combination of mutation–accumulation experiments and high-throughput sequencing enabled the estimation of mutation rates in most model organisms, but several major eukaryotic lineages remain unexplored. Here, we report the first estimation of the spontaneous mutation rate in a model unicellular eukaryote from the Stramenopile kingdom, the diatom Phaeodactylum tricornutum (strain RCC2967). We sequenced 36 mutation accumulation lines for an average of 181 generations per line and identified 156 de novo mutations. The base substitution mutation rate per site per generation is μbs = 4.77 × 10−10 and the insertion–deletion mutation rate is μid = 1.58 × 10−11. The mutation rate varies as a function of the nucleotide context and is biased toward an excess of mutations from GC to AT, consistent with previous observations in other species. Interestingly, the mutation rates between the genomes of organelles and the nucleus differ, with a significantly higher mutation rate in the mitochondria. This confirms previous claims based on indirect estimations of the mutation rate in mitochondria of photosynthetic eukaryotes that acquired their plastid through a secondary endosymbiosis. This novel estimate enables us to infer the effective population size of P. tricornutum to be Ne∼8.72 × 106.

scholarly journals Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines

2009 ◽  
Vol 19 (7) ◽  
pp. 1195-1201 ◽  
Author(s):  
P. D. Keightley ◽  
U. Trivedi ◽  
M. Thomson ◽  
F. Oliver ◽  
S. Kumar ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Spontaneous Mutation ◽  
Mutation Accumulation ◽  
Genome Sequences

scholarly journals Spontaneous Mutation Accumulation inDaphnia pulexin Selection-Free vs. Competitive Environments

2016 ◽  
Vol 34 (1) ◽  
pp. 160-173 ◽  
Author(s):  
Jullien M. Flynn ◽  
Frédéric J.J. Chain ◽  
Daniel J. Schoen ◽  
Melania E. Cristescu
Keyword(s):  
Spontaneous Mutation ◽  
Mutation Accumulation ◽  
Competitive Environments

scholarly journals Direct estimation of the spontaneous mutation rate by short-term mutation accumulation lines in Chironomus riparius

2016 ◽  
Author(s):  
Ann-Marie Oppold ◽  
Markus Pfenninger
Keyword(s):  
Mutation Rate ◽  
De Novo ◽  
Spontaneous Mutation ◽  
Single Point ◽  
Point Mutations ◽  
Mutation Accumulation ◽  
Occurrence Rate ◽  
Spontaneous Mutation Rate ◽  
Biting Midge ◽  
Mutational Spectrum

AbstractMutations are the ultimate basis of evolution, yet their occurrence rate is known only for few species. We directly estimated the spontaneous mutation rate and the mutational spectrum in the non-biting midge C. riparius with a new approach. Individuals from ten mutation accumulation lines over five generations were deep genome sequenced to count de novo mutations (DNMs) that were not present in a pool of F1 individuals, representing parental genotypes. We identified 51 new single site mutations of which 25 were insertions or deletions and 26 single point mutations. This shift in the mutational spectrum compared to other organisms was explained by the high A/T content of the species. We estimated a haploid mutation rate of 2.1 x 10−9 (95% confidence interval: 1.4 x 10−9 – 3.1 x 10−9) which is in the range of recent estimates for other insects and supports the drift barrier hypothesis. We show that accurate mutation rate estimation from a high number of observed mutations is feasible with moderate effort even for non-model species.

scholarly journals A broad mutational target explains an evolutionary trend

2019 ◽  
Author(s):  
Fabrice Besnard ◽  
Joao Picao-Osorio ◽  
Clément Dubois ◽  
Marie-Anne Félix
Keyword(s):  
Cell Fate ◽  
Mutation Rate ◽  
Tandem Repeats ◽  
Spontaneous Mutation ◽  
Rapid Evolution ◽  
Mutation Accumulation ◽  
High Mutation Rate ◽  
Genetic Linkage Analysis ◽  
Evolutionary Trend ◽  
Mutational Variance

ABSTRACTAn evolutionary trend, the rapid evolution of a trait in a group of organisms, can in some cases be explained by the mutational variance, the propensity of a phenotype to change under spontaneous mutation. However, the causes of high mutational variance are still elusive. For some morphological traits, fast evolution was shown to depend on the high mutation rate of one or few underlying loci with short tandem repeats. Here, we investigate the case of the fastest evolving cell fate among vulva precursor cells in Caenorhabditis nematodes, that of the cell called ‘P3.p’. For this, we combine mutation accumulation lines, whole-genome sequencing, genetic linkage analysis of the phenotype in recombinant lines, and candidate testing through mutant and CRISPR genome editing to identify causal mutations and the corresponding loci underlying the high mutational variance of P3.p. We identify and validate molecular lesions responsible for changes in this cell’s phenotype during a mutation accumulation experiment. We find that these loci do not present any characteristics of a high mutation rate, are scattered across the genome and belong to distinct biological pathways. Our data instead indicate that a broad mutational target size is the cause of the high mutational variance and of the corresponding evolutionary trend.

scholarly journals EFFECTS OF SPONTANEOUS MUTATION ACCUMULATION ON SEX RATIO TRAITS IN A PARASITOID WASP

Evolution ◽  
2008 ◽  
Vol 62 (8) ◽  
pp. 1921-1935 ◽  
Author(s):  
Bart A. Pannebakker ◽  
Daniel L. Halligan ◽  
K. Tracy Reynolds ◽  
Gavin A. Ballantyne ◽  
David M. Shuker ◽  
...  
Keyword(s):  
Sex Ratio ◽  
Spontaneous Mutation ◽  
Parasitoid Wasp ◽  
Mutation Accumulation
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