Evolution Of A Key Innovation In E-Coli

My thanks for the link to the e-coli long-term evolutionary experiment, aka LTEE.
[emphasis in all text is by me].

This experiment, begun in 1988 and still progressing, was designed to watch for long term evolutionary activity in colonies of e-coli that were begun from identical clones:

“The founding strain is strictly asexual, and thus populations have evolved by natural selection and genetic drift acting on variation generated solely by spontaneous mutations that occurred during the experiment. Thus, the LTEE allows us to examine the effects of contingency that are inherent to the core evolutionary processes of mutation, selection, and drift.”

The environmental inducement to adapt is the use of a citrate in the plate, along with a very limited amount of the normal nutrient. E-coli are known to be able to use citrate as a nutrient once it is inside the cell, but lack a functional transport mechanism to bring it in from the outside. So in an environment high in citrate but low in normal nutrient, will the e-coli evolve a mechanism to transport the more available nutrient?

After more than 33,000 generations and “billions of mutations” , strains of Cit+ e-coli were found, and the colonies became dominant, although sharing the plates with original Cit- e-coli colonies.

The experiment was designed with built-in replicability by having frozen samples of the cultures at every 500 generations. This allowed the experimenters to “rerun” the experiment through the development of the Cit+ strain, to see if it would repeat. If it did repeat, it would mean that a prior, “historical” event must have been present. The Cit+ strain did, in fact, appear in the repeated experiments. This means that even with a different mutation experience, the Cit+ strain appearance was inevitable in these colonies.

The authors' interpretation of the follow-on experiments is that there must have been an “historical-contingency” type of prior event, probably followed by at least two rare mutations that evoked or enabled the transport of the citrate into the cell.

“The deviations from the null expectations range from marginally to highly significant in the three experiments, and in all cases they support the historical-contingency hypothesis, according to which clones from later generations have greater propensity to evolve the Cit+ phenotype”

Which means that:

“These analyses compel us to reject the hypothesis that a rare mutation could have produced a Cit+ variant with equal probability at any point in the LTEE.

“Our results instead support the hypothesis of historical contingency, in which a genetic background arose that had an increased potential to evolve the Cit+ phenotype.”

“What physiological mechanism has evolved that allows aerobic growth on citrate? E. coli should be able to use citrate as an energy source after it enters the cell, but it lacks a citrate transporter that functions in an oxygen-rich environment. One possibility is that the Cit+ lineage activated a ‘‘cryptic’’ transporter (41), that is, some once-functional gene that has been silenced by mutation accumulation. This explanation seems unlikely to us because the Cit+ phenotype is characteristic of the entire species, one that is very diverse and therefore very old. We would expect a cryptic gene to be degraded beyond recovery after millions of years of disuse. A more likely possibility, in our view, is that an existing transporter has been coopted for citrate transport under oxic conditions. This transporter may previously have transported citrate under anoxic conditions (43) or, alternatively, it may have transported another substrate in the presence of oxygen. The evolved changes might involve gene regulation, protein structure, or both (61).

“In any case, our study shows that historical contingency can have a profound and lasting impact under the simplest, and thus most stringent, conditions in which initially identical populations evolve in identical environments. Even from so simple a beginning, small happenstances of history may lead populations along different evolutionary paths. A potentiated cell took the one less traveled by, and that has made all the difference.”

Conclusion:
The results are therefore indeterminate in the sense of knowing whether a new feature has been developed, or a long dormant one has been re-enabled, epigenetically. Until this is resolved, the appellation “evolution” – in the long-term, new feature, new creature sense – is not yet appropriate. The use of “evolution” to cover any change whatsoever is the sense in which it seems to be used here. I don't agree that it is less parsimonious to assume that a dormant gene is being revived; I think that testing should be done first, and conclusions drawn later.

This is a well designed experiment that deserves watching as new sub-experiments are designed and implemented, and as more definitive DNA analysis resolves the issue of what the Cit+ mechanism actually consists.