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

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. The generation game An experiment in which a lab population of Escherichia coli has been growing with glucose as a limiting nutrient for almost 20 years has provided an opportunity to examine the tempo and mode of genomic evolution. Genomes of E. coli clones were sampled after 2,000, 5,000, 10,000, 15,000, 20,000 and 40,000 generations. Adaptation decelerated sharply, but genomic evolution was nearly constant for 20,000 generations. Such regularity is considered characteristic of neutral evolution, but several lines of evidence indicate that most of these mutations were beneficial. The population later evolved an elevated mutation rate and accumulated hundreds of additional mutations dominated by a neutral signature. Clearly, the coupling between genomic and adaptive evolution is a complex matter. Here, in order to gain insight into the relationship between rates of genomic evolution and organismal adaptation, genomes sampled through 40,000 generations are sequenced from a laboratory population of Escherichia coli . The results indicate that the coupling between genomic and adaptive evolution is complex and can be counterintuitive even in a constant environment, with beneficial mutations surprisingly uniform over time whereas neutral substitutions were highly variable.