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17 results for “Evolution of mutation rates”
Data from: Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution
<p>The study "Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution" by Schenk et al. explores the phenotypic and genotypic changes in <em>Escherichia coli </em>after 500 generations of laboratory adaptation to increasing concentrations of an antibiotic (CTX). The source data files and scripts pertaining to the figures in the main manuscript and the extended data are available on the publishers webiste. Here we provide the source data files and scripts pertaining to the supplementary materials, organized according the figures in the supplementary material. Data are provided for Figures S2-S4, S6-S8, and S10-S12.</p>
Data from: Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution
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Divergent evolution of mutation rates and biases in the long-term evolution experiment with Escherichia coli
Abstract All organisms encode enzymes that replicate, maintain, pack, recombine, and repair their genetic material. For this reason, mutation rates and biases also evolve by mutation, variation, and natural selection. By examining metagenomic time series of the Lenski long-term evolution experiment (LTEE) with Escherichia coli (Good, et al. 2017), we find that local mutation rate variation has evolved during the LTEE. Each LTEE population has evolved idiosyncratic differences in their rates of point mutations, indels, and mobile element insertions, due to the fixation of various hypermutator and antimutator alleles. One LTEE population, called Ara+3, shows a strong, symmetric wave pattern in its density of point mutations, radiating from the origin of replication. This pattern is largely missing from the other LTEE populations, most of which evolved missense, indel, or structural mutations in topA, fis, and dusB— loci that all affect DNA topology. The distribution of mutations in those genes over time suggests epistasis and historical contingency in the evolution of DNA topology, which may have in turn affected local mutation rates. Overall, the replicate populations of the LTEE have largely diverged in their mutation rates and biases, even though they have adapted to identical abiotic conditions.
Divergent evolution of mutation rates and biases in the long-term evolution experiment with Escherichia coli
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Data from: Evolution of mutation rates in hypermutable populations of Escherichia coli propagated at very small effective population size
Mutation is the ultimate source of the genetic variation—including variation for mutation rate itself—that fuels evolution. Natural selection can raise or lower the genomic mutation rate of a population by changing the frequencies of mutation rate modifier alleles associated with beneficial and deleterious mutations. Existing theory and observations suggest that where selection is minimized, rapid systematic evolution of mutation rate either up or down is unlikely. Here, we report systematic evolution of higher and lower mutation rates in replicate hypermutable Escherichia coli populations experimentally propagated at very small effective size—a circumstance under which selection is greatly reduced. Several populations went extinct during this experiment, and these populations tended to evolve elevated mutation rates. In contrast, populations that survived to the end of the experiment tended to evolve decreased mutation rates. We discuss the relevance of our results to current ideas about the evolution, maintenance and consequences of high mutation rates.
Data from: A trade-off between oxidative stress resistance and DNA repair plays a role in the evolution of elevated mutation rates in bacteria
The dominant paradigm for the evolution of mutator alleles in bacterial populations is that they spread by indirect selection for linked beneficial mutations when bacteria are poorly adapted. In this paper, we challenge the ubiquity of this paradigm by demonstrating that a clinically important stressor, hydrogen peroxide, generates direct selection for an elevated mutation rate in the pathogenic bacterium Pseudomonas aeruginosa as a consequence of a trade-off between the fidelity of DNA repair and hydrogen peroxide resistance. We demonstrate that the biochemical mechanism underlying this trade-off in the case of mutS is the elevated secretion of catalase by the mutator strain. Our results provide the first experimental evidence that direct selection can favour mutator alleles in bacterial populations, and pave the way for future studies to understand how mutation and DNA repair are linked to stress responses and how this impacts the evolution of bacterial mutation rates.
Data from: The effect of bacterial mutation rate on the evolution of CRISPR-Cas adaptive immunity
CRISPR-Cas immune systems are present in around half of bacterial genomes. Given the specificity and adaptability of this immune mechanism, it is perhaps surprising that they are not more widespread. Recent insights into the requirement for specific host factors for the function of some CRISPR-Cas subtypes, as well as the negative epistasis between CRISPR-Cas and other host genes, have shed light on potential reasons for the partial distribution of this immune strategy in bacteria. In this study, we examined how mutations in the bacterial mismatch repair system, which are frequently observed in natural and clinical isolates and cause elevated host mutation rates, influence the evolution of CRISPR-Cas–mediated immunity. We found that hosts with a high mutation rate very rarely evolved CRISPR-based immunity to phage compared to wild-type hosts. We explored the reason for this effect and found that the higher frequency at which surface mutants pre-exist in the mutator host background causes them to rapidly become the dominant phenotype under phage infection. These findings suggest that natural variation in bacterial mutation rates may, therefore, influence the distribution of CRISPR-Cas adaptive immune systems.
Data from: Elevated mutation rates underlie the evolution of the aquatic plant family Podostemaceae
<p>Molecular evolutionary rates vary among lineages and influence the evolutionary process. Here, we report elevated genome-wide mutation rates in Podostemaceae, a family of aquatic plants with a unique body plan that allows members to live on submerged rocks in fast-flowing rivers. Molecular evolutionary analyses using 1,640 orthologous gene groups revealed two historical increases in evolutionary rates: the first at the emergence of the family and the second at the emergence of Podostemoideae, which is the most diversified subfamily. In both branches, synonymous substitution rates were elevated, indicating higher mutation rates. On early branches, mutations were biased in favour of AT content, which is consistent with a role for ultraviolet light-induced mutation and a habitat shift. In ancestors of Podostemoideae, DNA-repair genes were enriched in genes under positive selection, which may have responded to the meristem architectural changes.</p>
Data from: Mutation rate evolution in partially selfing and partially asexual organisms
Different factors may influence the evolution of the mutation rate of a species: costs associated with DNA replication fidelity, indirect selection caused by the mutations produced (that should generally favor lower mutation rates, given that most mutations affecting fitness are deleterious) and genetic drift, that may render selection acting on weak mutators inefficient. In this paper, we use a two-locus model to compute the strength of indirect selection acting on a modifier locus that affects the mutation rate towards a deleterious allele at a second, linked locus, in a population undergoing partial selfing or partial clonality. The results show that uniparental reproduction increases the effect of indirect selection for lower mutation rates. Extrapolating to the case of a whole genome with many deleterious alleles and introducing a direct cost a DNA replication fidelity, the results can be used to compute the evolutionarily stable mutation rate U. In the absence of mutational bias towards higher U, the analytical prediction fits well with individual-based, multilocus simulation results. When such a bias is added into the simulations, however, genetic drift may lead to the maintenance of higher mutation rates, and this effect may be amplified in highly selfing or highly clonal populations due to their reduced effective population size.
Data from: The effect of population bottlenecks on mutation rate evolution in asexual populations
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Data from: Mutation rate evolution in partially selfing and partially asexual organisms
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Data from: The effect of bacterial mutation rate on the evolution of CRISPR-Cas adaptive immunity
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Data from: Evolution of mutation rates in hypermutable populations of Escherichia coli propagated at very small effective population size
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Data from: A trade-off between oxidative stress resistance and DNA repair plays a role in the evolution of elevated mutation rates in bacteria
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Data from: The evolution of bacterial mutation rates under simultaneous selection by inter-specific and social parasitism
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Data from: Elevated mutation rates underlie the evolution of the aquatic plant family Podostemaceae
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The evolution of low mutation rates in experimental mutator populations of Saccharomyces cerevisiae
GEO Series GSE35440. Saccharomyces cerevisiae. 9 samples. Type: Expression profiling by array.
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