Analysis of 264 complete genomes from 12 E coli populations … in a 50,000-generation experiment

Anyone who thinks that ‘evolution is not going on, around us, all the time’ … needs to revise his/her thinking. The Lenski lab in 1988 (at Michigan State) began a carefully-controlled experiment with bacteria (E. coli) growing on a defined medium ‘with scarce resources’––thereby causing ‘constant environmental stress’ on the bacteria, which was expected to ‘force the bugs’ to adapt to their stressor environment in order to survive and produce subsequent generation(s). Since their generation time (‘doubling time’) is ~28 min, compared with that for mouse (~6 weeks) or human (20-25 years), E. coli provide a fantastic means for studying adaptive changes over many generation times. The Lenski lab (lucky to have had continuous federal funding for 28 years so far) has now surpassed 50,000 generations and, more recently, with whole-genome sequencing (WGS) now readily available at reasonable cost, they have now [see attached] analyzed 264 complete genomes of these bacteria (as a function of time over those 50,000 generations).

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. The authors 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.

Authors also compared these populations to mutation-accumulation lines evolved under a bottlenecking regimen that minimizes selection. Nonsynonymous mutations (those in the DNA that cause an amino-acid change), intergenic mutations (between genes), insertions and deletions are over-epresented in the long-term populations––further supporting the inference that most mutations that reached high frequency are chosen by selection. These very cool results therefore illuminate the shifting balance of forces that govern genome evolution in populations adapting to a new environment.

Tenaillon et al., Nature  11 Aug 2o16; 536: 165–170

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