ArticleGenetics2015
Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli.
Article in Genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers, 1 of them a synthesis that pooled it.
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Who cites it
94 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Coexistence Theory for Microbial Ecology, and Vice Versa.Environmental microbiology · 2025Pooled it
- Parallel evolution of chimeric genes in microbial evolution experiments.Microbial genomics · 2026Article
- Experimental evolution in an era of molecular manipulation.Nature reviews. Genetics · 2026Review
- An experimental outlook on investigating temporal-scale dynamics of microbial communities.ISME communications · 2026Article
- Substantial deceleration of adaptation of HIV-1 within 1500 generations in an experimental evolution: a genomic perspective.Virus evolution · 2026Article
- Bacterial mutation dynamics emerging insights into virulence evolution and drug resistance. A review study.Frontiers in medicine · 2026Review
- The balance between intrinsic and ecological fitness reveals hidden regimes in eco-evolutionary population dynamics.Research square · 2025Article
- The balance between intrinsic and ecological fitness reveals hidden regimes in eco-evolutionary population dynamics.bioRxiv : the preprint server for biology · 2025Article
- Adaptive genetics reveals constraints on protein structure/function by evolving E. coli under constant nutrient limitation.BMC biology · 2025Article
- Scaling laws of bacterial and archaeal plasmids.Nature communications · 2025Article
- The evolution of thermal performance curves in response to rising temperatures across the model genus yeast.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Detecting (the Absence of) Species Interactions in Microbial Ecological Systems.Studies in applied mathematics (Cambridge, Mass.) · 2025Article
- Article
- Tautology explains evolution without variation and selection. A Comment on: 'An evolutionary process without variation and selection' (2021), by GaboraJournal of the Royal Society, Interface · 2024Article
- Effects of periodic bottlenecks on the dynamics of adaptive evolution in microbial populations.Microbiology (Reading, England) · 2024Article
- Genomic sequencing reveals convergent adaptation during experimental evolution in two budding yeast species.Communications biology · 2024Article
- The distribution of beneficial mutational effects between two sister yeast species poorly explains natural outcomes of vineyard adaptation.bioRxiv : the preprint server for biology · 2024Article
- Wild Patagonian yeast improve the evolutionary potential of novel interspecific hybrid strains for lager brewing.PLoS genetics · 2024Article
- Correlated Allele Frequency Changes Reveal Clonal Structure and Selection in Temporal Genetic Data.Molecular biology and evolution · 2024Article
- Adaptive evolution of plasmid and chromosome contributes to the fitness of a blaNDM-bearing cointegrate plasmid in Escherichia coli.The ISME journal · 2024Article
34 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Twelve replicate populations of Escherichia coli have been evolving in the laboratory for >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, two genetically diverged clades coexisted for >6000 generations before one went extinct. In that time, many additional mutations arose in the clade that eventually prevailed. We show that the clades evolved a frequency-dependent interaction, which prevented the immediate competitive exclusion of either clade, but which 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.
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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.