ArticleProceedings of the National Academy of Sciences of the United States of America2006
Tests of parallel molecular evolution in a long-term experiment with Escherichia coli.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 186 papers, 3 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
186 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Machine learning enables prediction of metabolic system evolution in bacteria.Science advances · 2023Pooled it
- Pooled it
- The probability of genetic parallelism and convergence in natural populations.Proceedings. Biological sciences · 2012Pooled it
- The genetic foundations of convergent traits.Nature reviews. Genetics · 2026Review
- Conserved rod-to-spherical shape transitions in Escherichia coli through primordial experimental adaptations.Bioscience reports · 2026Article
- Uniform bacterial genetic diversity along the gut.Nature communications · 2026Article
- Article
- Substantial deceleration of adaptation of HIV-1 within 1500 generations in an experimental evolution: a genomic perspective.Virus evolution · 2026Article
- Mutations Elevate an Underground Pathway to a Physiologically Relevant Protopathway.Molecular biology and evolution · 2025Article
- Parallel evolution of salinity tolerance inScience advances · 2025Article
- Resource presentation dictates genetic and phenotypic adaptation in yeast.BMC ecology and evolution · 2025Article
- Enriching productive mutational paths accelerates enzyme evolution.Nature chemical biology · 2024Article
- Environmental memory alters the fitness effects of adaptive mutations in fluctuating environments.Nature ecology & evolution · 2024Article
- Effect of Plasma-Activated Water on the Cellulase-Producing StrainJournal of fungi (Basel, Switzerland) · 2024Article
- Genomics of hybrid parallel origin in Aquilegia ecalcarata.BMC ecology and evolution · 2024Article
- Proteome partitioning constraints in long-term laboratory evolution.Nature communications · 2024Article
- Trade-offs, trade-ups, and high mutational parallelism underlie microbial adaptation during extreme cycles of feast and famine.Current biology : CB · 2024Article
- A synthetic methylotrophicNature catalysis · 2024Article
- Convergent genetic adaptation ofFrontiers in molecular biosciences · 2024Article
- Linking genotypic and phenotypic changes in theeLife · 2023Article
126 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
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The repeatability of evolutionary change is difficult to quantify because only a single outcome can usually be observed for any precise set of circumstances. In this study, however, we have quantified the frequency of parallel and divergent genetic changes in 12 initially identical populations of Escherichia coli that evolved in identical environments for 20,000 cell generations. Unlike previous analyses in which candidate genes were identified based on parallel phenotypic changes, here we sequenced four loci (pykF, nadR, pbpA-rodA, and hokB/sokB) in which mutations of unknown effect had been discovered in one population, and then we compared the substitution pattern in these "blind" candidate genes with the pattern found in 36 randomly chosen genes. Two candidate genes, pykF and nadR, had substitutions in all 11 other populations, and the other 2 in several populations. There were very few cases, however, in which the exact same mutations were substituted, in contrast to the findings from conceptually related work performed with evolving virus populations. No random genes had any substitutions except in four populations that evolved defects in DNA repair. Tests of four different statistical aspects of the pattern of molecular evolution all indicate that adaptation by natural selection drove the parallel changes in these candidate genes.
Indexed as
Identifiers
What OpenQuestion holds
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.