Genome evolution and adaptation in a long-term experiment with Escherichia coli
Abstract
The relationship between rates of genomic evolution and organismal adaptation remains uncertain, despite considerable interest. The feasibility of obtaining genome sequences from experimentally evolving populations offers the opportunity to investigate this relationship with new precision. Here we sequence genomes sampled through 40,000 generations from a laboratory population of Escherichia coli. Although adaptation decelerated sharply, genomic evolution was nearly constant for 20,000 generations. Such clock-like regularity is usually viewed as the signature of neutral evolution, but several lines of evidence indicate that almost all of these mutations were beneficial. This same population later evolved an elevated mutation rate and accumulated hundreds of additional mutations dominated by a neutral signature. Thus, the coupling between genomic and adaptive evolution is complex and can be counterintuitive even in a constant environment. In particular, beneficial substitutions were surprisingly uniform over time, whereas neutral substitutions were highly variable.
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Due to transcriptional profiling and massive next-generation DNA sequencing, phenotype-genotype correlations can be easily obtained by whole genome re-sequencing.
“Moreover, due to rather new technologies, including transcriptional profiling [30] and massive next-generation DNA sequencing (NGS) [31,32], phenotype-genotype correlations can be easily obtained by whole genome re-sequencing (WGS).”
From Adaptive laboratory evolution—Principles and applications for biotechnology (2013) · cites this paper as [32]
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- Authors
- Barrick, J. E., Yu, D. S., Yoon, S. H., Jeong, H., Oh, T. K., Schneider, D., Lenski, R. E., & Kim, J. F.
- Affiliations
- Michigan State University (US)
- Chungnam National University (KR)
- Korea Research Institute of Bioscience and Biotechnology (KR)
- Centre National de la Recherche Scientifique (FR)
- Corresponding author
- Lenski, Richard E.
- Kim, Jihyun F.
- ORCID
- Venue
- Nature
- Published
- 2009-10
- Volume
- 461
- Issue
- 7268
- Pages
- 1243-1247
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2031581341
- Cited by
- 1,184
- References
- 58
- Citations by year
- 2026: 22 · 2025: 38 · 2024: 58 · 2023: 58 · 2022: 41 · 2021: 44 · 2020: 46 · 2019: 69 · 2018: 62 · 2017: 82 · 2016: 84 · 2015: 96 · 2014: 95 · 2013: 110 · 2012: 103
- FWCI
- 53.71
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- KRIBB Repository (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Social Sciences › Cultural Studies › Language and cultural evolution
- Social Sciences › Arts and Humanities › History and Philosophy of Science › Philosophy and History of Science
- Keywords
- genome evolution, adaptation, Escherichia coli, long-term evolution experiment, beneficial mutations, mutation rate, glucose limitation, tempo and mode of evolution, neutral evolution, adaptive evolution
- MeSH terms
- Adaptation, Physiological, DNA Mutational Analysis, Escherichia coli, Models, Genetic, Mutation, Selection, Genetic, Time Factors, Genome, Bacterial, Evolution, Molecular, Genetic Fitness
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