Tuesday, August 9, 2016

LTEE - E.coli and long term evolution - Lenski and his E coli

The E.coli long-term evolution experiment is an experiment started in 1988, which has been continued for more than 65,000 generations now. Changes in fitness, evolution of new phenotypes and the associated changes in the genome have been monitored for 12 initially identical populations that have now diverged. We recently discussed the analysis of a dataset spanning 50,000 generations that showed an abundance of non-synonymous over synonymous changes. Even after 50,000 generations "beneficial" (non-synonymous) changes outnumber the synonymous changes. 

Re-plotting the data provided in the paper, we see a clear pattern of non-synonymous/synonymous >1 for the non-mutator populations with a peak at around 20,000 generations, followed by a decline. The point mutator populations have the opposite pattern with more synonymous changes than non-synonymous changes. 

The plot below shows a clear difference in the rate of accumulation of mutations between the "mutator" and non-mutator strains. Both these patterns are noted in the paper and are used to make say "Our experimental results thus support a selectionist view of molecular evolution, complementing indirect evidence based on comparative genomics in bacteria, Drosophila and humans. Of course, the LTEE may differ from many natural populations in important respects including its low mutation rate, the absence of sex or horizontal gene transfer, and a stable environment. As we showed, high mutation rates tend to obscure the role of selection in molecular evolution."

Just to pretend that i found something new in the data, i plot the G-score (which is used to assess the degree of parallelism between clones) across the genome. In the below figure, it looks like we have a cluster of high G-scores between 3,248,576 and 3,481,685. This cluster has 7 of the 15 highest G-score genes reported in the Table-1. Although not consecutive genes, this pattern does seem a bit striking.