Gas station without pumps

2011 March 27

Evolvability wins

Filed under: Uncategorized — gasstationwithoutpumps @ 09:09
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There has been a nice story about the benefits of evolvability lately, coming out of an old experiment at Michigan State that managed to get a Science article (Second-Order Selection for Evolvability in a Large Escherichia coli Population. Robert J. Woods, Jeffrey E. Barrick,Tim F. Cooper, Utpala Shrestha, Mark R. Kauth, Richard E. Lenski). Note: that link gets to the paper without a paywall.

The basic experiment is simple: E. coli were evolved for a very long time (> 50,000 generations) under fixed conditions, until one strain had been heavily optimized by evolution for those conditions.  Then clones from early stages of the experiment (500, 1000, and 1500 generations) were checked for mutations that had been found to be beneficial (that is, that had gone to fixation in the population fairly rapidly: by around 1500 generations).  There was a fair amount of diversity in the 500-generation pool, so they picked 4 strains to work with: 2 that had the “eventual winner”  (EW) mutations and 2 that did not (EL). The interesting thing was that the EW strains had less fitness than the EL strains:  that is the strains that eventually won were initially less fit.

They converted each strain into two very similar ones, by introducing a marker mutation that (they claimed) were not relevant to fitness under these conditions, and let each strain evolve (asexually) again. The started with equal amounts of marked and unmarked copies of one strain, and followed the ratio of marked to unmarked cells every 20 generations for about 880 generations.  The did this in 10 populations of each of the 4 strains, making 40 total populations being tracked.  They fit a simple evolution model to the trajectories: a 2-parameter model that has a rate of beneficial mutations and a fitness effect for the mutations, together with a competition model.

The model fitting showed that the EW strains evolved faster, but that even the first beneficial mutation did not make them more fit than the EL strains, though there did not appear to do any head-to-head comparisons with early strains, but only with the strains after beneficial mutations had swept to fixation at 880 generations.  By that time, the EW strains had a 2% fitness advantage over the EL strains, despite their weaker starts. “We stress, however, that this result is necessarily probabilistic in nature. Not every evolved EW clone was able to outcompete every evolved EL clone.”

The sequenced 2 evolved strains from each of the 4 strains they started with and found 2–5 new mutations in each.  There was no evidence for greater mutation rates in the EW strains.  The observed a total 0f 16 mutations in the 4 sequenced EW strains and 15 in 4 EL strains.  They analyzed the mutations and conjecture that mutations in the pykF and spoT genes were primarily responsible for the EW advantages.  They did further experiments that showed that the spoT mutations were beneficial when added to the EW2 background, but not when added to the EL1 background.  They further isolated the difference to different alleles of the topA gene:

The EL topA1 allele is beneficial on its own, though less so than the EW topA mutation. The spoT mutation is also highly beneficial on its own and has essentially the same fitness effect in the presence of the EW topA allele. By contrast, this spoT mutation is neutral, or at least much less beneficial, in combination with the EL topA1 mutation.

It is cool that the EL strains, despite their initial fitness advantage, evolved more slowly and eventually lost to the EW strains, and that the difference was traceable to epistatic effects, rather than changes in mutation rate.

In the press release, Lenski talks about the results in terms of games: “In games it makes sense to sacrifice some pieces for an eventual winning move. The eventual winners were able to overcome their short-term disadvantage over the course of several evolutionary moves by producing more beneficial mutations.”

In addition to the Science article, Lenski was also interviewed by NSF and got an article in the NY Times: E. Coli Bacteria Show Evolvability in Action.

1 Comment »

  1. […] Evolvability wins […]

    Pingback by Blogoversary « Gas station without pumps — 2011 June 5 @ 10:52 | Reply

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