Journal Article

Tempo and mode of genome evolution in a 50,000-generation experiment

Lenski, Richard E., Ribeck, Noah, Barrick, Jeffrey E., Wu, Gabriel C., Cruveiller, Stéphane, Blanchard, Jeffrey L., Schneider, Dominique, Tenaillon, Olivier, Médigue, Claudine, Deatherage, Daniel E., Dasgupta, Aurko, Wielgoss, Sébastien

2016

Overview

Adaptation by natural selection depends on the rates, effects and interactions of many mutations, making it difficult to determine what proportion of mutations in an evolving lineage are beneficial. Here we analysed 264 complete genomes from 12 Escherichia coli populations to characterize their dynamics over 50,000 generations. The populations that retained the ancestral mutation rate support a model in which most fixed mutations are beneficial, the fraction of beneficial mutations declines as fitness rises, and neutral mutations accumulate at a constant rate. We also compared these populations to mutation-accumulation lines evolved under a bottlenecking regime that minimizes selection. Nonsynonymous mutations, intergenic mutations, insertions and deletions are overrepresented in the long-term populations, further supporting the inference that most mutations that reached high frequency were favoured by selection. These results illuminate the shifting balance of forces that govern genome evolution in populations adapting to a new environment. Whole-genome sequencing of 264 clones sampled from 12 Escherichia coli populations evolved over 50,000 generations under identical culture conditions is used to characterize the patterns and dynamics of genome evolution over time. Watching bacterial evolution Richard Lenski and colleagues report whole-genome sequencing of 264 clones sampled from 12 bacterial populations evolved over 50,000 generations under identical culture conditions as part of the project known as the Escherichia coli long-term evolution experiment, which has been under way since 1988. The authors characterize the patterns and dynamics of genome evolution over time, including the rate of neutral and beneficial mutation accumulation, in this uniquely controlled experimental system.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/181/2474 / 631/181/2475 / 631/326/325/2482 / Adaptation / Bacteria / Biodiversity / Cloning / E coli / Escherichia coli / Escherichia coli - genetics / Escherichia coli - physiology / Escherichia coli Proteins - genetics / Evolution & development / Evolution, Molecular / Evolutionary genetics / Experiments / Gene mutations / Genes / Genes, Bacterial - genetics / Genetic aspects / Genetic Loci - genetics / Genome, Bacterial - genetics / Genomes / Humanities and Social Sciences / Identification and classification / Life Sciences / Methods / Models, Genetic / multidisciplinary / Mutation / Mutation Rate / Natural history / Phylogenetics / Phylogeny / Population / Populations and Evolution / Reproduction, Asexual - genetics / Science / Selection, Genetic - genetics / Time Factors