The outcomes of evolution are determined by a stochastic dynamical process that governs how mutations arise and spread through a population. However, it is difficult to observe these dynamics directly over long periods and across entire genomes. Here we analyse the dynamics of molecular evolution in twelve experimental populations of Escherichia coli, using whole-genome metagenomic sequencing at five hundred-generation intervals through sixty thousand generations. Although the rate of fitness gain declines over time, molecular evolution is characterized by signatures of rapid adaptation throughout the duration of the experiment, with multiple beneficial variants simultaneously competing for dominance in each population. Interactions between ecological and evolutionary processes play an important role, as long-term quasi-stable coexistence arises spontaneously in most populations, and evolution continues within each clade. We also present evidence that the targets of natural selection change over time, as epistasis and historical contingency alter the strength of selection on different genes. Together, these results show that long-term adaptation to a constant environment can be a more complex and dynamic process than is often assumed. Using data from sixty thousand generations of the E. coli long-term evolution experiment, the authors shed new light on the processes that govern molecular evolution. The Escherichia coli long-term evolution experiment (LTEE) is the longest running bacterial evolution experiment, including 12 replicate populations of E. coli serially propagated for more than 60,000 generations. Michael Desai, Richard Lenski and colleagues now report whole-genome sequencing at 500-generation intervals over the course of the 60,000 generations from the LTEE. Their analyses reveal a complex and dynamic evolutionary process of long-term bacterial adaptation in this controlled environment, and include findings on clonal inference, genetic drift and shifting targets of selection.

The dynamics of molecular evolution over 60,000 generations