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Genome evolution and adaptation in a long-term experiment with Escherichia coli

Author

Listed:
  • Jeffrey E. Barrick

    (Michigan State University, East Lansing, Michigan 48824, USA)

  • Dong Su Yu

    (Industrial Biotechnology and Bioenergy Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong, Daejeon 305-806, Korea
    Chungnam National University, Yuseong, Daejeon 305-764, Korea)

  • Sung Ho Yoon

    (Industrial Biotechnology and Bioenergy Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong, Daejeon 305-806, Korea)

  • Haeyoung Jeong

    (Industrial Biotechnology and Bioenergy Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong, Daejeon 305-806, Korea)

  • Tae Kwang Oh

    (Industrial Biotechnology and Bioenergy Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong, Daejeon 305-806, Korea
    21C Frontier Microbial Genomics and Applications Center, Yuseong, Daejeon 305-806, Korea)

  • Dominique Schneider

    (Institut Jean Roget, Laboratoire Adaptation et Pathogénie des Microorganismes, CNRS UMR 5163, Université Joseph Fourier, Grenoble 1, BP 170, F-38042 Grenoble cedex 9, France)

  • Richard E. Lenski

    (Michigan State University, East Lansing, Michigan 48824, USA)

  • Jihyun F. Kim

    (Industrial Biotechnology and Bioenergy Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong, Daejeon 305-806, Korea
    Functional Genomics Program, School of Science, University of Science and Technology, Yuseong, Daejeon 305-333, Korea)

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.

Suggested Citation

  • Jeffrey E. Barrick & Dong Su Yu & Sung Ho Yoon & Haeyoung Jeong & Tae Kwang Oh & Dominique Schneider & Richard E. Lenski & Jihyun F. Kim, 2009. "Genome evolution and adaptation in a long-term experiment with Escherichia coli," Nature, Nature, vol. 461(7268), pages 1243-1247, October.
  • Handle: RePEc:nat:nature:v:461:y:2009:i:7268:d:10.1038_nature08480
    DOI: 10.1038/nature08480
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    Cited by:

    1. Ida Lauritsen & Pernille Ott Frendorf & Silvia Capucci & Sophia A. H. Heyde & Sarah D. Blomquist & Sofie Wendel & Emil C. Fischer & Agnieszka Sekowska & Antoine Danchin & Morten H. H. Nørholm, 2021. "Temporal evolution of master regulator Crp identifies pyrimidines as catabolite modulator factors," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    2. Simeon D. Castle & Michiel Stock & Thomas E. Gorochowski, 2024. "Engineering is evolution: a perspective on design processes to engineer biology," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    3. Matteo Mori & Vadim Patsalo & Christian Euler & James R. Williamson & Matthew Scott, 2024. "Proteome partitioning constraints in long-term laboratory evolution," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    4. Linyue Zhang & Edward King & William B. Black & Christian M. Heckmann & Allison Wolder & Youtian Cui & Francis Nicklen & Justin B. Siegel & Ray Luo & Caroline E. Paul & Han Li, 2022. "Directed evolution of phosphite dehydrogenase to cycle noncanonical redox cofactors via universal growth selection platform," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    5. Ryo Mizuuchi & Taro Furubayashi & Norikazu Ichihashi, 2022. "Evolutionary transition from a single RNA replicator to a multiple replicator network," Nature Communications, Nature, vol. 13(1), pages 1-10, December.

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