Mutation supply and the repeatability of selection for antibiotic resistance.

@article{vanDijk2017MutationSA,
  title={Mutation supply and the repeatability of selection for antibiotic resistance.},
  author={Thomas van Dijk and Sungmin Hwang and Joachim H A Krug and J. Arjan G.M. de Visser and Mark P. Zwart},
  journal={Physical biology},
  year={2017},
  volume={14 5},
  pages={
          055005
        }
}
Whether evolution can be predicted is a key question in evolutionary biology. Here we set out to better understand the repeatability of evolution, which is a necessary condition for predictability. We explored experimentally the effect of mutation supply and the strength of selective pressure on the repeatability of selection from standing genetic variation. Different sizes of mutant libraries of antibiotic resistance gene TEM-1 β-lactamase in Escherichia coli, generated by error-prone PCR… 

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References

SHOWING 1-10 OF 48 REFERENCES
Quantifying the Adaptive Potential of an Antibiotic Resistance Enzyme
TLDR
The distribution of mutation effects on cefotaxime (Ctx) resistance and fitness of 48 unique beneficial mutations in the bacterial enzyme TEM-1 β-lactamase is studied, finding that the distribution of both measures follows a Fréchet-type distribution characterized by a broad tail of a few exceptionally fit mutants.
Patterns of Epistasis between Beneficial Mutations in an Antibiotic Resistance Gene
Understanding epistasis is central to biology. For instance, epistatic interactions determine the topography of the fitness landscape and affect the dynamics and determinism of adaptation. However,
The Molecular Diversity of Adaptive Convergence
TLDR
The pervasive presence of epistasis among beneficial mutations was inferred, which shaped adaptive trajectories into at least two distinct pathways involving mutations either in the RNA polymerase complex or the termination factor rho.
Initial Mutations Direct Alternative Pathways of Protein Evolution
TLDR
It is found that a combination of decreased enzymatic activity and lower folding cooperativity underlies negative sign epistasis in the clash between key mutations in the common and deviating lines, demonstrating that epistasis contributes to contingency in protein evolution by amplifying the selective consequences of random mutations.
Divergent evolution peaks under intermediate population bottlenecks during bacterial experimental evolution
TLDR
The hypothesis that bottleneck intensity shapes parallel evolution is tested by elucidating the genomic basis of adaptation to antibiotic-supplemented media in hundreds of populations of the bacterium Pseudomonas fluorescens Pf0-1, demonstrating that population bottlenecking can be a major predictor of parallel evolution, but precisely how is more complex than many simple theoretical predictions.
Global epistasis makes adaptation predictable despite sequence-level stochasticity
TLDR
Results show that beneficial mutations affecting a variety of biological processes are globally coupled; they interact strongly, but only through their combined effect on fitness, which follows a predictable trajectory even though sequence-level adaptation is stochastic.
Stick Insect Genomes Reveal Natural Selection’s Role in Parallel Speciation
Stick to the Bush Can the underlying genetic changes driving the divergence of populations into new species be predicted or repeated? Soria-Carrasco et al. (p. 738) investigated the genetic changes
Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins
TLDR
It is demonstrated that 102 mutational trajectories linking β-lactamase alleles are inaccessible to Darwinian selection and that many of the remaining trajectories have negligible probabilities of realization, which implies that the protein tape of life may be largely reproducible and even predictable.
The Innate Growth Bistability and Fitness Landscapes of Antibiotic-Resistant Bacteria
TLDR
A quantitative phenomenological model is formulated to predict the growth rates of drug-resistant strains in the presence of drugs, based on the well-characterized biochemistry of drug and drug-resistance interactions and on bacterial growth laws that dictate relations between cell growth and gene expression, which reveals a plateau-like fitness landscape.
The fate of competing beneficial mutations in an asexual population
TLDR
The beneficial mutation rate and the distribution of mutational effects from changes in mean fitness in an evolving E. coli population are estimated.
...
...