Genomic evolution during a 10,000-generation experiment with bacteria

Papadopoulos, Dimitri; Schneider, Dominique; Meier-Eiss, Jessica; Arber, Werner; Lenski, Richard E.; Blot, Michel

doi:10.1073/pnas.96.7.3807

Cited by 234Evolution and Genetic DynamicsGenomics and Phylogenetic StudiesChromosomal and Genetic Variations

Genomic evolution during a 10,000-generation experiment with bacteria

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Papadopoulos, Dimitri, Schneider, Dominique, Meier-Eiss, Jessica, Arber, Werner, Lenski, Richard E., Blot, Michel·1999·Proceedings of the National Academy of Sciences

DOI 10.1073/pnas.96.7.3807PMC PMC22376

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Abstract

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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So far there has been little evidence to support the proposition that the overall rate of adaptation or morphological change of a species might influence the molecular clock.
“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]
Given the lack of a relationship between phenotypic evolution and molecular rates, 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.
“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.”
From The modern molecular clock (2003) · cites this paper as [19]

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Authors: Papadopoulos, D., Schneider, D., Meier-Eiss, J., Arber, W., Lenski, R. E., & Blot, M.
Affiliations: Centre National de la Recherche Scientifique (FR)
ORCID: Papadopoulos, Dimitri
Schneider, Dominique
Lenski, Richard E.
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
DOI: 10.1073/pnas.96.7.3807
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 › Agricultural and Biological Sciences › Plant Science › 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

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Genomic evolution during a 10,000-generation experiment with bacteria

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