ArticleNature ecology & evolution2020
Chromosomal barcoding of E. coli populations reveals lineage diversity dynamics at high resolution.
Article in Nature ecology & evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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42 citing papers in PubMed, 74 citations in OpenAlex.
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- Direct estimation of genotype fitness from time series.bioRxiv : the preprint server for biology · 2026Article
- Functional diversity of phage sponge proteins that sequester host immune signals.Nature microbiology · 2026Article
- Longitudinal lineage tracing reveals early clonal attrition during Drosophila midgut aging.PLoS biology · 2026Article
- Broadly conserved protective epitopes on the lyme disease vaccine antigen, OspA.PLoS pathogens · 2026Article
- Putting BASIL in a BLT: A Bayesian filtering method for estimating the fitness effects of nascent adaptive mutations.PLoS computational biology · 2026Article
- Contrasting pH optima of β-lactamases CTX-M and CMY influenceApplied and environmental microbiology · 2026Article
- Quantifying host-microbe interactions with bacterial lineage tracing.Science (New York, N.Y.) · 2026Review
- Experimental evolution in an era of molecular manipulation.Nature reviews. Genetics · 2026Review
- Doblin: inferring dominant clonal lineages from high-resolution DNA barcoding time series.Bioinformatics (Oxford, England) · 2025Article
- A widespread family of viral sponge proteins reveals specific inhibition of nucleotide signals in anti-phage defense.Molecular cell · 2025Article
- Quantifying the intra- and inter-species community interactions in microbiomes by dynamic covariance mapping.Nature communications · 2025Article
- Quantitative measurement of phenotype dynamics during cancer drug resistance evolution using genetic barcoding.Nature communications · 2025Article
- Precise lineage tracking using molecular barcodes demonstrates fitness trade-offs for ivermectin resistance in nematodes.G3 (Bethesda, Md.) · 2025Article
- AInfection and immunity · 2025Article
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- The Mla pathway promotesmBio · 2025Article
- Design and regulation of engineered bacteria for environmental release.Nature microbiology · 2025Review
- ORBIT for E. coli: kilobase-scale oligonucleotide recombineering at high throughput and high efficiency.Nucleic acids research · 2024Article
- Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags.Nature microbiology · 2024Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Evolutionary dynamics in large asexual populations is strongly influenced by multiple competing beneficial lineages, most of which segregate at very low frequencies. However, technical barriers to tracking a large number of these rare lineages in bacterial populations have so far prevented a detailed elucidation of evolutionary dynamics. Here, we overcome this hurdle by developing a chromosomal-barcoding technique that allows simultaneous tracking of approximately 450,000 distinct lineages in Escherichia coli, which we use to test the effect of sub-inhibitory concentrations of common antibiotics on the evolutionary dynamics of low-frequency lineages. We find that populations lose lineage diversity at distinct rates that correspond to their antibiotic regimen. We also determine that some lineages have similar fates across independent experiments. By analysing the trajectory dynamics, we attribute the reproducible fates of these lineages to the presence of pre-existing beneficial mutations, and we demonstrate how the relative contribution of pre-existing and de novo mutations varies across drug regimens. Finally, we reproduce the observed lineage dynamics by simulations. Altogether, our results provide a valuable methodology for studying bacterial evolution as well as insights into evolution under sub-inhibitory antibiotic levels.
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