What happens in 60,000 generations of evolution?

Mike McDonald, working with colleagues from the United States, has found that long-term adaptation to a constant environment can be a more complex and dynamic process than is often assumed.

The team were able to observe this process directly by using frozen samples of E. coli from the ongoing experimental evolution study led by Richard Lenski, now in its 30th year. This is over 67,000 generations for each of the 12 replicate populations.

This figure shows the trajectories of different mutations in different populations. A mutation may become ‘fixed’ where 100% of all alleles have that mutation, others may reach substantial frequencies before becoming extinct. What was most striking however was when neither fixation or extinction occurred, with 9 of the 12 populations maintaining 2 or more stable “subpopulations”, within the culture. This indicates that one way the populations can continue to adapt for so long is by diversifying and evolving niche specific subpopulations.

Previous studies have shown that the populations have not yet reached the expected ‘fitness peak’ despite tens of thousands of generations in the same environment.  While the competitive fitness of each generation continues to increase, the rate of improvement has slowed. Through analysing genome sequences every 500 generations, Mike and the research team have been able to analyse when, and in what order, successful mutations occur, the dynamics by which they spread through a population and what other competing mutations have arisen.

Their data revealed a complex adaptive process with competition between lineages arising from different beneficial mutations important, but genetic drift and eco-evolutionary feedback also playing significant roles. In the latter instance the evolving E. coli change the environment they are growing in, which can, in turn, influence the evolutionary trajectories of the different populations.

The combination of such processes can help explain why the rate of molecular evolution in E. coli populations remains so high through 60,000 generations.

These results help us understand the complex population genetic processes that take place in the long term adaptation to a fixed environment and are in stark contrast to the ‘evolutionary desert’ expected near a fitness peak.

This research has been published in the journal Nature.