Blount ZD, Barrick JE, Davidson CJ, Lenski RE. (2012) Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 489:513-8. doi: 10.1038/nature11514
Richard Lenski is conducting an experiment called the long-term evolution experiment (LTEE) in which twelve populations of E. coli are grown in a glucose-limited minimal medium. This experiment has now been running for over 40,000 generations (>20 years). If we take a human generation as being 25 years, this is equivalent to one million years of Homo evolution.
One of the diagnostic traits of the species E. coli is the inability to grow aerobically on citrate. The medium that is used in the LTEE does however contain citrate as a chelating agent (probably to solubilise ferric ions, although I haven't been able to confirm this). The Lenski group have recently reported on the appearance of a novel citrate-utilising mutant in one of the populations. The Cit+ variant appeared at around 31000 generations, and became dominant after 33000 generations. Because the LTEE involves storing samples of each population every 500 generations it has been possible to analyse in detail the emergence of this new phenotypic trait, and indeed to replay it.
The process that they describe has three phases:
1) Potentiation. This stage involved the appearance of mutations that were a necessary prerequisite for subsequent events. In this case it is thought that there were at least two potentiating mutations. These are as yet unidentified but their existence is inferred from replay experiments.
2) Actualization. This is the emergence of the new trait, and in this case is the event that took place at 31,000 generations. This involved a tandem duplication event at the citT locus, bringing citT under control of a new promoter, belonging to the rnk gene. The citT protein is a citrate transporter that is only expressed under anaerobic conditions in wild-type E. coli. The gene duplication event led to the expression of the transporter under standard aerobic conditions, opening up the possibility of taking up citrate and metabolising it. Replay experiments indicate that this event originally conferred a very weak Cit+ phenotype.
3) Refinement. This involves changes that strengthen the Cit+ phenotype. In this case these seem to have been further gene duplications of the rnk-citT module (with up to eight copies in one replay experiment). This eventually stabilised with the presence of four copies.
This may be the nearest that we can hope to get to defining a timeline of evolution of a new characteristic.