scholarly journals Tempo and mode of genome evolution in a 50,000-generation experiment

2016 ◽  
Author(s):  
Olivier Tenaillon ◽  
Jeffrey E. Barrick ◽  
Noah Ribeck ◽  
Daniel E. Deatherage ◽  
Jeffrey L. Blanchard ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genome Evolution ◽  
Mutation Rate ◽  
Beneficial Mutations ◽  
Insertions And Deletions ◽  
Constant Rate ◽  
Shifting Balance ◽  
Balance Of Forces ◽  
Neutral Mutations

Adaptation depends on the rates, effects, and interactions of many mutations. We analyzed 264 genomes from 12 Escherichia coli populations to characterize their dynamics over 50,000 generations. The trajectories for genome evolution in populations that retained the ancestral mutation rate fit a model where most fixed mutations are beneficial, the fraction of beneficial mutations declines as fitness rises, and neutral mutations accumulate at a constant rate. We also compared these populations to lines evolved under a mutation-accumulation regime that minimizes selection. Nonsynonymous mutations, intergenic mutations, insertions, and deletions are overrepresented in the long-term populations, supporting the inference that most fixed mutations are favored by selection. These results illuminate the shifting balance of forces that govern genome evolution in populations adapting to a new environment.

Genome evolution and adaptation in a long-term experiment with Escherichia coli

Nature ◽  
2009 ◽  
Vol 461 (7268) ◽  
pp. 1243-1247 ◽  
Author(s):  
Jeffrey E. Barrick ◽  
Dong Su Yu ◽  
Sung Ho Yoon ◽  
Haeyoung Jeong ◽  
Tae Kwang Oh ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genome Evolution ◽  
Term Experiment ◽  
Long Term Experiment

scholarly journals Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli

2015 ◽  
Author(s):  
Rohan Maddamsetti ◽  
Richard E. Lenski ◽  
Jeffrey E. Barrick
Keyword(s):  
Escherichia Coli ◽  
Frequency Dependence ◽  
Evolutionary Dynamics ◽  
Selective Sweeps ◽  
Clonal Interference ◽  
Beneficial Mutations ◽  
Frequency Dependent ◽  
Evolution Experiment ◽  
History Of

Twelve replicate populations of Escherichia coli have been evolving in the laboratory for more than 25 years and 60,000 generations. We analyzed bacteria from whole-population samples frozen every 500 generations through 20,000 generations for one well-studied population, called Ara???1. By tracking 42 known mutations in these samples, we reconstructed the history of this population???s genotypic evolution over this period. The evolutionary dynamics of Ara???1 show strong evidence of selective sweeps as well as clonal interference between competing lineages bearing different beneficial mutations. In some cases, sets of several mutations approached fixation simultaneously, often conveying no information about their order of origination; we present several possible explanations for the existence of these mutational cohorts. Against a backdrop of rapid selective sweeps both earlier and later, we found that two clades coexisted for over 6000 generations before one drove the other extinct. In that time, at least nine mutations arose in the clade that prevailed. We found evidence that the clades evolved a frequency-dependent interaction, which prevented the competitive exclusion of either clade, but which eventually collapsed as beneficial mutations accumulated in the clade that prevailed. Clonal interference and frequency dependence can occur even in the simplest microbial populations. Furthermore, frequency dependence may generate dynamics that extend the period of coexistence that would otherwise be sustained by clonal interference alone.

scholarly journals Escherichia coli with a Tunable Point Mutation Rate for Evolution Experiments

2020 ◽  
Vol 10 (8) ◽  
pp. 2671-2681 ◽  
Author(s):  
Nicholas A. Sherer ◽  
Thomas E. Kuhlman
Keyword(s):  
Escherichia Coli ◽  
Point Mutation ◽  
Mutation Rate ◽  
Fitness Landscape ◽  
Genetically Engineered ◽  
Mutation Rates ◽  
Nucleotide Polymorphisms ◽  
Beneficial Mutations ◽  
Beneficial Effects ◽  
Evolution Experiment

The mutation rate and mutations’ effects on fitness are crucial to evolution. Mutation rates are under selection due to linkage between mutation rate modifiers and mutations’ effects on fitness. The linkage between a higher mutation rate and more beneficial mutations selects for higher mutation rates, while the linkage between a higher mutation rate and more deleterious mutations selects for lower mutation rates. The net direction of selection on mutations rates depends on the fitness landscape, and a great deal of work has elucidated the fitness landscapes of mutations. However, tests of the effect of varying a mutation rate on evolution in a single organism in a single environment have been difficult. This has been studied using strains of antimutators and mutators, but these strains may differ in additional ways and typically do not allow for continuous variation of the mutation rate. To help investigate the effects of the mutation rate on evolution, we have genetically engineered a strain of Escherichia coli with a point mutation rate that can be smoothly varied over two orders of magnitude. We did this by engineering a strain with inducible control of the mismatch repair proteins MutH and MutL. We used this strain in an approximately 350 generation evolution experiment with controlled variation of the mutation rate. We confirmed the construct and the mutation rate were stable over this time. Sequencing evolved strains revealed a higher number of single nucleotide polymorphisms at higher mutations rates, likely due to either the beneficial effects of these mutations or their linkage to beneficial mutations.

scholarly journals Benefits of a Recombination-Proficient Escherichia coli System for Adaptive Laboratory Evolution

2016 ◽  
Vol 82 (22) ◽  
pp. 6736-6747 ◽  
Author(s):  
George Peabody ◽  
James Winkler ◽  
Weston Fountain ◽  
David A. Castro ◽  
Enzo Leiva-Aravena ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Strong Support ◽  
Mutational Load ◽  
Adaptive Laboratory Evolution ◽  
Beneficial Mutations ◽  
Laboratory Evolution ◽  
Content Type ◽  
Sexual Recombination ◽  
Simple Kinetic Model ◽  
Neutral Mutations

ABSTRACTAdaptive laboratory evolution typically involves the propagation of organisms asexually to select for mutants with the desired phenotypes. However, asexual evolution is prone to competition among beneficial mutations (clonal interference) and the accumulation of hitchhiking and neutral mutations. The benefits of horizontal gene transfer toward overcoming these known disadvantages of asexual evolution were characterized in a strain ofEscherichia coliengineered for superior sexual recombination (genderless). Specifically, we experimentally validated the capacity of the genderless strain to reduce the mutational load and recombine beneficial mutations. We also confirmed that inclusion of multiple origins of transfer influences both the frequency of genetic exchange throughout the chromosome and the linkage of donor DNA. We built a simple kinetic model to estimate recombination frequency as a function of transfer size and relative genotype enrichment in batch transfers; the model output correlated well with the experimental data. Our results provide strong support for the advantages of utilizing the genderless strain over its asexual counterpart during adaptive laboratory evolution for generating beneficial mutants with reduced mutational load.IMPORTANCEOver 80 years ago Fisher and Muller began a debate on the origins of sexual recombination. Although many aspects of sexual recombination have been examined at length, experimental evidence behind the behaviors of recombination in many systems and the means to harness it remain elusive. In this study, we sought to experimentally validate some advantages of recombination in typically asexualEscherichia coliand determine if a sexual strain ofE. colican become an effective tool for strain development.

scholarly journals Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli

2011 ◽  
Vol 1 (3) ◽  
pp. 183-186 ◽  
Author(s):  
Sébastien Wielgoss ◽  
Jeffrey E. Barrick ◽  
Olivier Tenaillon ◽  
Stéphane Cruveiller ◽  
Béatrice Chane-Woon-Ming ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Mutation Rate ◽  
Long Term Evolution ◽  
Synonymous Substitutions ◽  
Term Evolution ◽  
Evolution Experiment

scholarly journals Diverse phenotypic and genetic responses to short-term selection in evolving Escherichia coli populations

2015 ◽  
Author(s):  
Marcus M Dillon ◽  
Nicholas P Rouillard ◽  
Brian Van Dam ◽  
Romain Gallet ◽  
Vaughn S Cooper
Keyword(s):  
Escherichia Coli ◽  
Fitness Landscape ◽  
Single Point ◽  
Beneficial Mutations ◽  
True Nature ◽  
Term Selection ◽  
Adaptive Mutations ◽  
Fitness Effects ◽  
Genetic Responses

Beneficial mutations fuel adaptation by altering phenotypes that enhance the fit of organisms to their environment. However, the phenotypic effects of mutations often depend on ecological context, making the distribution of effects across multiple environments essential to understanding the true nature of beneficial mutations. Studies that address both the genetic basis and ecological consequences of adaptive mutations remain rare. Here, we characterize the direct and pleiotropic fitness effects of a collection of 21 first-step beneficial mutants derived from naive and adapted genotypes used in a long-term experimental evolution of Escherichia coli. Whole-genome sequencing was used to identify most beneficial mutations. In contrast to previous studies, we find diverse fitness effects of mutations selected in a simple environment and few cases of genetic parallelism. The pleiotropic effects of these mutations were predominantly positive but some mutants were highly antagonistic in alternative environments. Further, the fitness effects of mutations derived from the adapted genotypes were dramatically reduced in nearly all environments. These findings suggest that many beneficial variants are accessible from a single point on the fitness landscape, and the fixation of alternative beneficial mutations may have dramatic consequences for niche breadth reduction via metabolic erosion.

Sign in / Sign up

Export Citation Format

Share Document