The dynamics of molecular evolution during 60,000 generations of the Escherichia coli (E. coli) bacterium

After the recent sharing of a GEITP report about a bird’s beak “evolving” to become longer –– to accommodate decades of birdfeeders in the gardens of England –– here is another example of “Evolution in Action.” 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 et al. now report whole-genome sequencing (WGS) 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.

Evolutionary adaptation is driven by the accumulation of mutations, but the temporal dynamics of this process are difficult to observe directly. Recently, time-resolved sequencing of microbial evolution experiments, viral and bacterial infections, and cancers has begun to illuminate this process. These studies reveal complex dynamics, characterized by rapid adaptation, competition between beneficial mutations, diminishing-returns epistasis (gene-gene interactions), and extensive genetic parallelism. These forces can alter patterns of polymorphism and influence which mutations ultimately become fixed. However, it is unclear whether these dynamics are general, or, instead, reflect the short time-scales and novel environmental conditions of previous studies.

To address this question, authors [see attached report] turned to an experiment with the longest frozen ‘fossil record’: the E. coli LTEE. The twelve LTEE populations have been serially propagated in the same type of medium for more than 60,000 generations, with samples preserved every 500 generations. Previous work has shown that the competitive fitness of each population continues to increase through 60,000 generations, despite a decline in the rate of improvement. The genome sequences of evolved clones have shown that these fitness gains are accompanied by steady accumulation of mutations. Parallel genetic changes across replicate populations suggest that there is a common pool of adaptive mutations that has yet to be exhausted in any single population.

The outcomes of evolution are determined by a stochastic (randomly determined) dynamical process that governs how mutations arise and how they spread through a population.

Although the rate of fitness gain –– during these sixty thousand generations –– 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. Authors also provide 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 incredible results show that long-term adaptation to a constant environment can be a more complex and dynamic process than is often assumed..!!

Nature 2 Nov 2o17; 551: 45–50

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