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!
I like how many mutations happened in critical protein coding genes and yet, the bacterium is still there, doing better than ever.
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.
For those who don’t wish to read the whole thing, the short discussion hits on most of the important points:
(excuse the formatting–I’m too lazy to take out the reference numbers)
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.
Rumraket,
Take that genetic entropy.
And a lot of other claims.
Still no squirrels emerging from the Petri dishes, though.
But my local squirrel has once again mastered the impossible bird feeder. Took two weeks.
+∞
From the abstract:
and from Dave Carlson’s quote:
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.
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.
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.
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?
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):
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.
Paging genetic entropy guys. Will someone please calculate how many generations it will take for these populations to melt down?
I’m sure Sal can do that!
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’.
petrushka,
How many Lenski-generations you planning to stick around? It’s just beyond that.
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.
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.
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):
This may apply to only about half the mutator populations, however.
Ahh alright, thanks.
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.
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.
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!
Dave Carlson,
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.
Alan:
No, not at all, and Lenski et al don’t think so either:
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.
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.
Fair enough.
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!
The interview is from Lenski’s blog, this is the last part:
https://telliamedrevisited.wordpress.com/2015/02/26/funding-the-ltee-past-present-and-future-questions-from-jeremy-fox-about-the-ltee-part-4/
The one I saw was with David Sloan Wilson as the interviewer: “Evolutionary Biology’s Master Craftsman: An Interview with Richard Lenski.”
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.
When you Google genetic draft, it asks if you meant genetic drift …
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.
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.
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.
That would be the physical basis of the hitchhiking.
No?
They have been programmed to search for a target phrase.
Does the paper offer an objective way to measure cumulative selection?
Laughing at the Lenski Weasel, no doubt.
Post a link to the OP in which you set forth Wagner’s thesis and offered to defend it.
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.
Tom English,
Designer is an artist – no two strokes the same 😉
I understand.
Yep. Hitchhiking results in linkage disequilibrium between alleles, while recombination breaks up that association between them.