ArticleGenetics2013
Synchronous waves of failed soft sweeps in the laboratory: remarkably rampant clonal interference of alleles at a single locus.
Article in Genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
31 citing papers in PubMed, 78 citations in OpenAlex.
- Mutation-biased adaptation is consequential even in large bacterial populations.Nature communications · 2026Article
- Article
- Cryptic phenotypic variation emerges rapidly during the adaptive evolution of a carbapenemase.Nature ecology & evolution · 2026Article
- Mutational Switch-Backs Can Accelerate Evolution ofFrontiers in microbiology · 2022Article
- Polygenic Adaptation and Clonal Interference Enable Sustained Diversity in Experimental Pseudomonas aeruginosa Populations.Molecular biology and evolution · 2021Article
- Genetic Context Significantly Influences the Maintenance and Evolution of Degenerate Pathways.Genome biology and evolution · 2021Article
- Substitutions Are Boring: Some Arguments about Parallel Mutations and High Mutation Rates.Trends in genetics : TIG · 2019Review
- Identification of parallel and divergent optimization solutions for homologous metabolic enzymes.Metabolic engineering communications · 2018Article
- Parallel Evolution of High-Level Aminoglycoside Resistance inFrontiers in microbiology · 2018Article
- Local Fitness Landscapes Predict Yeast Evolutionary Dynamics in Directionally Changing Environments.Genetics · 2018Article
- Mutator genomes decay, despite sustained fitness gains, in a long-term experiment with bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Population Parameters Underlying an Ongoing Soft Sweep in Southeast Asian Malaria Parasites.Molecular biology and evolution · 2017Article
- High-Throughput Identification of Adaptive Mutations in Experimentally Evolved Yeast Populations.PLoS genetics · 2016Article
- Large-Effect Beneficial Synonymous Mutations Mediate Rapid and Parallel Adaptation in a Bacterium.Molecular biology and evolution · 2016Article
- Antisense Transcription of Retrotransposons in Drosophila: An Origin of Endogenous Small Interfering RNA Precursors.Genetics · 2016Article
- Love the one you're with: replicate viral adaptations converge on the same phenotypic change.PeerJ · 2016Article
- Competition and fixation of cohorts of adaptive mutations under Fisher geometrical model.PeerJ · 2016Article
- Elucidating the molecular architecture of adaptation via evolve and resequence experiments.Nature reviews. Genetics · 2015Review
- Article
- Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli.Genetics · 2015Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
It has increasingly been recognized that adapting populations of microbes contain not one, but many lineages continually arising and competing at once. This process, termed "clonal interference," alters the rate and dynamics of adaptation and biases winning mutations toward those with the largest selective effect. Here we uncovered a dramatic example of clonal interference between multiple similar mutations occurring at the same locus within replicate populations of Methylobacterium extorquens AM1. Because these mutational events involved the transposition of an insertion sequence into a narrow window of a single gene, they were both readily detectable at low frequencies and could be distinguished due to differences in insertion sites. This allowed us to detect up to 17 beneficial alleles of this type coexisting in a single population. Despite conferring a large selective benefit, the majority of these alleles rose and then fell in frequency due to other lineages emerging that were more fit. By comparing allele-frequency dynamics to the trajectories of fitness gains by these populations, we estimated the fitness values of the genotypes that contained these mutations. Collectively across all populations, these alleles arose upon backgrounds with a wide range of fitness values. Within any single population, however, multiple alleles tended to rise and fall synchronously during a single wave of multiple genotypes with nearly identical fitness values. These results suggest that alleles of large benefit arose repeatedly in failed "soft sweeps" during narrow windows of adaptation due to the combined effects of epistasis and clonal interference.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.