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

Jeffrey E. Barrick, Dong Su Yu, Sung Ho Yoon, Haeyoung Jeong, Tae Kwang Oh, Dominique Schneider, Richard E. Lenski () and Jihyun F. Kim ()
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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
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
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

Nature, 2009, vol. 461, issue 7268, 1243-1247

Abstract: 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.

Date: 2009
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DOI: 10.1038/nature08480

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