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Genomic evolution during a 10,000-generation experiment with bacteria
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Molecular methods are used widely to measure genetic diversity within populations and determine relationships among species. However, it is difficult to observe genomic evolution in action because these dynamics are too slow in most organisms. To overcome this limitation, we sampled genomes from populations of Escherichia coli evolving in the laboratory for 10,000 generations. We analyzed the genomes for restriction fragment length polymorphisms (RFLP) using seven insertion sequences (IS) as probes; most polymorphisms detected by this approach reflect rearrangements (including transpositions) rather than point mutations. The evolving genomes became increasingly different from their ancestor over time. Moreover, tremendous diversity accumulated within each population, such that almost every individual had a different genetic fingerprint after 10,000 generations. As has been often suggested, but not previously shown by experiment, the rates of phenotypic and genomic change were discordant, both across replicate populations and over time within a population. Certain pivotal mutations were shared by all descendants in a population, and these are candidates for beneficial mutations, which are rare and difficult to find. More generally, these data show that the genome is highly dynamic even over a time scale that is, from an evolutionary perspective, very brief.
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“Although it is possible that the overall rate of adaptation or morphological change of a species might influence the molecular clock, so far there has been little evidence to support this proposition from either experimental studies 19 or comparative analyses 20,21 .”
From The modern molecular clock (2003) · cites this paper as [19]
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“Given the lack of a relationship between phenotypic evolution and molecular rates 19-21 , it seems unlikely that the observed faster rate of molecular evolution in more rapidly diversifying lineages is a result of species adapting to new niches.”
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Metadata
- Authors
- Papadopoulos, D., Schneider, D., Meier-Eiss, J., Arber, W., Lenski, R. E., & Blot, M.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 1999-03-30
- Volume
- 96
- Issue
- 7
- Pages
- 3807-3812
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC22376
- OpenAlex
- W2049065348
- Cited by
- 234
- References
- 39
- Citations by year
- 2026: 1 · 2023: 4 · 2022: 5 · 2021: 4 · 2020: 7 · 2019: 3 · 2018: 6 · 2017: 4 · 2016: 4 · 2015: 4 · 2014: 9 · 2013: 5 · 2012: 10
- FWCI
- 10.56
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Keywords
- genome evolution, Escherichia coli, restriction fragment length polymorphism, insertion sequences, transposition, genome rearrangement, genetic diversity, beneficial mutations, genome dynamics
- MeSH terms
- Cell Division, Escherichia coli, Biological Evolution, Models, Genetic, Phylogeny, Time, Genome, Bacterial
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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