Dynamics of genome evolution in E. coli

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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. I like how many mutations happened in critical protein coding genes and yet, the bacterium is still there, doing better than ever.

  2. Rumraket,

    Indeed. It’s interesting how they note that while the rate of fitness increase in later generations has declined relative to the early parts of the experiment, a large fraction of observed mutations appear to be adaptive even in later generations.

  3. For those who don’t wish to read the whole thing, the short discussion hits on most of the important points:

    Adaptation by natural selection sits at the heart of phenotypic evolution. However, the random processes of spontaneous mutation and genetic drift often overwhelm and obscure genomic signatures of adaptation. We overcame this difficulty by analysing genomes from 12 bacterial populations that evolved for 50,000 generations under identical culture conditions. Even so, six populations evolved hypermutable phenotypes that increased point-mutation rates ~100-fold, and another evolved hypermutability caused by a transposable element. By focusing on populations that retained the ancestral mutation rate, we identified several key features of the tempo and mode of their genome evolution. First, a population-genetic model with two terms—one for beneficial drivers, the other for neutral hitchhikers—fits the dynamics much better than models without both terms. Second, the great majority of mutations observed during the early generations were beneficial drivers. Third, the proportion of observed mutations that were beneficial declined over time but remained substantial even after 50,000 generations. The second and third findings follow from the population-genetic model. Both are also strongly supported by the excess of nonsynonymous to synonymous substitutions in the LTEE and by the excess of several classes of mutations, including indels, in comparison to mutation-accumulation lines. Fourth, there was strong gene-level parallel evolution across the replicate LTEE populations.

    Our analyses also show a contrast between the contributions of beneficial mutations to molecular evolution and to the fitness trajectory in a stable environment. In particular, beneficial mutations continued to constitute a large fraction of genetic changes throughout the 50,000 generations of the LTEE, whereas the resulting fitness gains were only a few per cent in the last 10,000 generations17. Beneficial mutations with very small selection coefficients are nonetheless visible to natural selection17. Hence, adaptation can remain a major driver of molecular evolution long after an environmental shift. Our experimental results thus support a selectionist view of molecular evolution, complementing indirect evidence based on comparative genomics in bacteria, Drosophila and humans45, 46, 47. Of course, the LTEE may differ from many natural populations in important respects including its low mutation rate, the absence of sex or horizontal gene transfer, and a stable environment. As we showed, high mutation rates tend to obscure the role of selection in molecular evolution. The effects of horizontal gene transfer48 and variable environments49, 50 on the dynamic coupling of genomic and adaptive evolution should also be examined further. Long-term experiments with microorganisms provide opportunities for rigorous analyses of these issues.

    (excuse the formatting–I’m too lazy to take out the reference numbers)

  4. Here ya go. Weasel in real life.

    And yes, the bacteria simply ignored the fact that functional islands are isolated, and walked on water to get to new functional sequences. Proof that there’s a divine hand tossing the dice.

  7. But my local squirrel has once again mastered the impossible bird feeder. Took two weeks.

  8. petrushka: And yes, the bacteria simply ignored the fact that functional islands are isolated, and walked on water to get to new functional sequences. Proof that there’s a divine hand tossing the dice.

    +∞

  9. From the abstract:

    …further supporting the inference that most mutations that reached high frequency were favoured by selection.

    and from Dave Carlson’s quote:

    In particular, beneficial mutations continued to constitute a large fraction of genetic changes throughout the 50,000 generations of the LTEE, whereas the resulting fitness gains were only a few per cent in the last 10,000 generations17. Beneficial mutations with very small selection coefficients are nonetheless visible to natural selection17. Hence, adaptation can remain a major driver of molecular evolution long after an environmental shift.

    A nail in the coffin of drift?

  10. Alan Fox:
    A nail in the coffin of drift?

    While these results are cool and important (IMHO), I wouldn’t extrapolate that far.

    Edit: Nevermind, I misread something.

  11. Well Joe F has been saying for some time that selection is sensitive to very small increments of benefit. He’s said this here and at Sandwalk.

    The last time gpuccio turned up here arguing for artificial selection (the designer’s hand on the dice) I argued that only an omniscient designer could do that.

    But drift as a percentage of mutation is still dominant, because most of the [human] genome is not conserved. If you are using genomes for determining lineages, non-conserved sequences would seem ideal.

  12. I think Lenski is cool, but am wary of many extrapolations. They are investigating tempo and mode in a particular, rather static, environment. Which is fine, and useful, but – for example – there appears to be selection ‘for’ a mutator phenotype. It has arisen 6 times independently, and I’d say a legitimate extrapolation is that it will happen in all eventually. This is interesting because it shows phenotypic convergence, and multiple genetic pathways thereto. But I suspect the spin doctors will use this to ‘show’ that evolution is impossible because of mutator phenotypes in ‘real’ experiments, just as they show mutation ‘invariably’ detrimental by reference to artificially accelerated populations.

  13. Where are our islands of function guys, the ones who won’t read Wagner, or who deny his thesis?

    Where are the needle in the haystack guys?

    Why do they not show up on Lenski threads?

  14. Allan Miller:
    I think Lenski is cool, but am wary of many extrapolations. They are investigating tempo and mode in a particular, rather static, environment. Which is fine, and useful, but – for example – there appears to be selection ‘for’ a mutator phenotype. It has arisen 6 times independently, and I’d say a legitimate extrapolation is that it will happen in all eventually. This is interesting because it shows phenotypic convergence, and multiple genetic pathways thereto. But I suspect the spin doctors will use this to ‘show’ that evolution is impossible because of mutator phenotypes in ‘real’ experiments, just as they show mutation ‘invariably’ detrimental by reference to artificially accelerated populations.

    I don’t think the bolded part above is actually very likely, given the following (note this is in the final version but not in the pre-print):

    Hypermutability tended to decline over time as the load of deleterious mutations favoured antimutator alleles. All four populations that were hypermutable at 10,000 generations accumulated synonymous substitutions (a proxy for the underlying point-mutation rate) between generations 40,000 and 50,000 at much lower rates than from 10,000 to 20,000 generations

    In any case, most of the analyses in the paper–specifically those looking at the proportion of substitutions likely to be adaptive–were performed on the non-mutator populations.

  15. Paging genetic entropy guys. Will someone please calculate how many generations it will take for these populations to melt down?

  16. petrushka: Will someone please calculate how many generations it will take for these populations to melt down?

    I’m sure Sal can do that!

  17. Dave Carlson,

    I don’t think the bolded part above is actually very likely, given the following (note this is in the final version but not in the pre-print):

    But why not? Although your quote shows mutability being disfavoured over the longer term, and there is selection for antagonists, it still doesn’t seem likely that 6 of 12 is just ‘chance’.

  19. Allan Miller:
    Dave Carlson,

    But why not? Although your quote shows mutability being disfavoured over the longer term, and there is selection for antagonists, it still doesn’t seem likely that 6 of 12 is just ‘chance’.

    I’m not saying that the evolution of mutator lines was just “chance”. However, from what I’ve read it seems like most (if perhaps not all) the instances of hyper mutability were advantageous fairly early on, and that there has been subsequent selection for a more “normal” mutation rate to reduce the negative effects of genetic load (see http://www.pnas.org/content/110/1/222.full). If this trend continues, I would not expect to see all 12 populations to end up as hypermutators.

  20. Allan Miller:
    petrushka,

    How many Lenski-generations you planning to stick around? It’s just beyond that.

    I’m beginning to wonder how many more Lenski-generations Lenksi is going to stick around! Hopefully somebody will take over once he retires. Also, I hope he writes a book.

  21. Do we know what the biochemical basis for hypermutability is in these populations? Is part of the detection and repair mechanism downregulated, or has it mutated so it’s less effective or.. ?

    For the later branches shown in green (clones 30K-A and 40K-A) and purple (clones 35K-C, 40K-B, and 40K-C), this rate had declined to 22 and 28 per thousand generations, respectively, which indicate reductions of ∼65% and ∼55%, respectively. However, the mutation in the mutT gene had not reverted to its ancestral state, even though that mutation was in a potentially mutable tract of five cytosines. </blockquote

    What does the mutT gene do? It's obviously related to controlling the mutation rate, but how?

  22. Rumraket:
    Do we know what the biochemical basis for hypermutability is in these populations? Is part of the detection and repair mechanism downregulated, or has it mutated so it’s less effective or.. ?

    Here’s what I found from an early Lenski paper (http://www.nature.com/nature/journal/v387/n6634/full/387703a0.html):

    To ascertain a genetic basis for the observed mutator phenotypes, we transformed 10,000-generation clonal isolates from populations Ara-2, Ara-4 and Ara+3, and an isolate from the ancestral strain REL606 with multicopy plasmids bearing wild-type alleles of seven known general mutator loci. The ancestral mutation rate was fully restored in the Ara-2, Ara-4 and Ara+3 strains only by the presence of wild-type alleles of genes in the methyl-directed mismatch repair pathway16 (Fig. 3). The mutation rate in the ancestral strain, REL606, was not significantly affected by the plasmids (with a single exception: see Fig. 3). In the Ara+3 strain the mutS+ allele alone restored the ancestral mutation rate. In the Ara-2 and Ara-4 strains the ancestral rate was restored completely by uvrD+, and the data also indicated a partial effect of mutL+. Recent studies have suggested that there is a mechanistic interaction between the mutL and uvrD gene products, such that a defect in one may in some cases be complemented by increased production of the other (P. Modrich, personal communication).

    This may apply to only about half the mutator populations, however.

  24. It occurs to me that this experiment is likely to be cloned and replicated elsewhere, sort of like the eternal cancer cell culture. I could envision a future in which Lenski kits are handed out to students as an exercise in laboratory technique.

    Or sold by Edmund Scientific for $19.95.

  25. petrushka: I could envision a future in which Lenski kits are handed out to students as an exercise in laboratory technique.

    I was just thinking that it’s going to get very interesting when this sort of work can be automated fully, and miniaturised. Much like the ‘lab in a briefcase’ and ‘lap on a chip’ revolution that is currently happening.

  26. Didn’t notice Dave’s link to the free paper and only just now read it quickly. I note the authors put “genetic drift” in italics!

  27. Dave Carlson,

    If this trend continues, I would not expect to see all 12 populations to end up as hypermutators.

    No, I wasn’t suggesting that was any kind of final destination. I said that it would ‘happen’, not that they would necessarily get stuck like that.

  28. Alan:

    A nail in the coffin of drift?

    No, not at all, and Lenski et al don’t think so either:

    Discussion

    Adaptation by natural selection sits at the heart of phenotypic evolution. However, the random processes of spontaneous mutation and genetic drift often overwhelm, or at least obscure, the genomic signatures of adaptation. We overcame this difficulty by combining a well-controlled experimental system with whole-genome sequencing.

  29. petrushka: Weasel in real life.

    The “intelligent design” propagandists tried to reduce the experiment to an attempt to get E. coli to digest citrate. That particular outcome is irrelevant to the paper. There’s nothing to be mistaken for a target. The LTEE gives evidence that evolution is radically contingent. All 12 lineages adapted, but no two of them adapted similarly.

  30. It will be fun to see what the folks ar ENV make of it.

    I’m betting none of our regulars will venture much of an opinion until moses comes down from the mountain.

  32. Dave Carlson: Hopefully somebody will take over once he retires.

    I read an interview of him recently (can’t recall where). He seemed confident that the experiment would continue long after he was gone.

  33. Tom English: I read an interview of him recently (can’t recall where). He seemed confident that the experiment would continue long after he was gone.

    That’s good news!

  36. Alan Fox:
    Didn’t notice Dave’s link to the free paper and only just now read it quickly. I note the authors put “genetic drift” in italics!

    Ah! My mistake! Genetic draft otherwise known as genetic hitchhiking.

  37. Alan Fox: Ah! My mistake! Genetic draft otherwise known as genetic hitchhiking.

    Yes, it is fairly common to see genetic draft used with quotation marks, which I take to be an acknowledgement that the term is awful, but is unfortunately probably here to stay.

  39. I think it has long been known that bits of unselected DNA hitchhike on larger pieces that are selected.

    What I read into this paper is that in the absence of large amounts and long sequences of non-functional DNA, everything is selected, either directly, or as a hitchhiker.

  40. petrushka: What I read into this paper is that in the absence of large amounts and long sequences of non-functional DNA, everything is selected, either directly, or as a hitchhiker.

    That was my impression. Hence my remark on drift, though I appreciate that drift is swamped in large populations under selective pressure and is (perhaps!) more relevant in eukaryotes.

  41. petrushka,

    The lack of recombination is a factor too. Entire genomes are competing for residence against other entire genomes, which is not the case in recombinant populations. The entire genome and everything in it is the ‘allele’ in this setup.

  43. petrushka: Here ya go. Weasel in real life.

    They have been programmed to search for a target phrase.

    Does the paper offer an objective way to measure cumulative selection?

  45. petrushka: Where are our islands of function guys, the ones who won’t read Wagner, or who deny his thesis?

    Post a link to the OP in which you set forth Wagner’s thesis and offered to defend it.

  47. I’ve wanted to start this discussion for several weeks, but wasn’t sure how to present Wagner’s argument. Fortunately Piotr has saved me the trouble with a post at UD.

  49. Mung: I’ve wanted to start this discussion for several weeks, but wasn’t sure how to present Wagner’s argument

    I understand.

  50. petrushka:
    That would be the physical basis of the hitchhiking.

    No?

    Yep. Hitchhiking results in linkage disequilibrium between alleles, while recombination breaks up that association between them.

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