Dynamics of genome evolution in E. coli

Hi All,

The Lenski lab has just published a new paper in Nature that looks at the dynamics of genome evolution in E. coli populations over the course of the LTEE.  Here is the abstract:

Tempo and mode of genome evolution in a 50,000-generation experiment

Adaptation by natural selection depends on the rates, effects and interactions of many mutations, making it difficult to determine what proportion of mutations in an evolving lineage are beneficial. Here we analysed 264 complete genomes from 12 Escherichia coli populations to characterize their dynamics over 50,000 generations. The populations that retained the ancestral mutation rate support a model in which most fixed mutations are beneficial, the fraction of beneficial mutations declines as fitness rises, and neutral mutations accumulate at a constant rate. We also compared these populations to mutation-accumulation lines evolved under a bottlenecking regime that minimizes selection. Nonsynonymous mutations, intergenic mutations, insertions and deletions are overrepresented in the long-term populations, further supporting the inference that most mutations that reached high frequency were favoured by selection. These results illuminate the shifting balance of forces that govern genome evolution in populations adapting to a new environment.

I’m assuming the whole thing is pay-walled, but a pre-print copy (which may or may not be identical to the final version) is freely available here.

I’ve only read the abstract thus far, but the paper seems likely to touch on a variety of topics that folks here like to discuss. Have at it!

64 thoughts on “Dynamics of genome evolution in E. coli

  1. You all are commenting on an ABSTRACT!?? Surely you must be joking.

    Don’t you realise right at this very moment Richard is having an asthmatic reaction? He in stammering and drooling all over himself, and calling for his wife to bring him a bedpan. he keeps yelling something about “keiths, keiths, help me….abstract, abstract,….oh lord, why is the room spinning so…DNA Jock, abstract! Not you too, Surely you won’t forsake me.”

  2. phoodoo,

    From the OP:

    I’m assuming the whole thing is pay-walled, but a pre-print copy (which may or may not be identical to the final version) is freely available here.

  3. keiths: All you had to do was read the OP, phoo.

    Yeah, phoo. Here it is for you in black and white:

    I’ve only read the abstract thus far…

  4. Mung: Yeah, phoo. Here it is for you in black and white:

    And I did read the whole thing eventually, even quoting much of it in the comments. What’s your point?

  5. Dave Carlson: What’s your point?

    That based on your own admission in the OP you were commenting on an abstract. That the fact that you provided a link to the paper is irrelevant to phoodoo’s claim that people were commenting on an abstract. It’s a red herring.

  6. Mung,

    I honestly have no idea what your comments (or Phoodoo’s for that matter) are referring to. Would you like to discuss the content of the paper?

  7. Dave Carlson: Would you like to discuss the content of the paper?

    Does it contain anything not already covered in T. Ryan Gregory’s The Evolution of The Genome? Any surprises? Anything previously unknown? Anything that overturns previously held beliefs?

  8. Mung,

    Having not read Gregory’s book, it seems like you’re in a better position to answer that question than I am. Why not read the paper and find out? As is the case with all Nature papers, it’s quite short.

    As for your other questions, the work is an excellent empirical data point to add to the debate regarding the extent to which molecular evolution tends to be driven more by selection or drift. In this particular case at least, selection seems to have the edge.

  9. Mung: Yeah, phoo. Here it is for you in black and white:

    Keith didn’t read that part. I think he was too busy reading the bible.

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