Lenski's E. Coli bacterial microevolution experiment
I have barely begun to read others' comments about the experiment, but here are my own observations and questions so far:
The mutations appear to have occurred at two or even three stages: the first -- or preliminary -- mutation at around the 27,000th generation (around the 20,000th generation according to some sources), the second at around the 31,500th generation, and possibly a third around the 33,000th generation.
Question: To what extent did the first mutation spread through the population, if it spread at all, considering that it apparently conferred no advantage?
There were around 44,000 generations in 20 years, or about 2,200 generations per year. So assuming that the first mutation occurred at 27,000 generations and the second occurred at 31,500 generations, that would be about 2 years from the first mutation until the second mutation. That seems to mean that the second mutation is rare -- however, on the other hand this second mutation appears to be common because it was repeated numerous times by starting with the unfrozen samples of previous generations. So how could the second mutation be both rare and common at the same time? Maybe the second mutation is really quite common but is rarely expressed because there are relatively few individuals with the first mutation, which confers no advantage.
Carl Zimmer said,
Blount took on the job of figuring out what happened. He first tried to figure out when it happened. He went back through the ancestral stocks to see if they included any citrate-eaters. For the first 31,000 generations, he could find none. Then, in generation 31,500, they made up 0.5% of the population. Their population rose to 19% in the next 1000 generations, but then they nearly vanished at generation 33,000. But in the next 120 generations or so, the citrate-eaters went berserk, coming to dominate the population.
Carl Zimmer gives the following explanation for the preceding observations:
This rise and fall and rise suggests that the evolution of citrate-eating was not a one-mutation affair. The first mutation (or mutations) allowed the bacteria to eat citrate, but they were outcompeted by some glucose-eating mutants that still had the upper hand. Only after they mutated further did their citrate-eating become a recipe for success.
Actually, the rise and fall at 31,500 and 33,000 generations respectively is not what indicates that the citrate-eating trait is not just a one-mutation affair, because -- as noted above -- it appears that an essential preliminary mutation occurred at around 27,000 generations (around 20,000 according to some sources).
Also, in a sense the citrate-eating bacteria are not really competing with the glucose-eating bacteria, because the two kinds of bacteria have different food sources.
The citrate-eaters were initially getting quite good at competing with the glucose-eaters, rising to 19% before nearly vanishing and then becoming dominant. Zimmer does not adequately explain why the citrate-eaters nearly vanished.
Also, Zimmer said,
Lenski started off with a single microbe. It divided a few times into identical clones, from which Lenski started 12 colonies. He kept each of these 12 lines in its own flask. Each day he and his colleagues provided the bacteria with a little glucose, which was gobbled up by the afternoon. The next morning, the scientists took a small sample from each flask and put it in a new one with fresh glucose. And on and on and on, for 20 years and running.
As I calculated above, there is an average of about 2,200 generations per year, so if a new population was started each day with a sample from an old population, then there were about 6 generations per population. With only 6 generations, there might be a significant possibility -- depending on the size of the sample -- that a mutation occurring in an old population would not be collected in the sample used to start the next population, particularly if the mutation occurred in one of the last generations of the old population. The populations should of course be well-stirred before collecting the samples to start the next populations - the Zimmer article says that the flasks full of E. coli were placed on a "gently rocking table," and I presume that means that the populations were well-stirred before collecting the samples.