Evolution of the Genetic Code

Continuing the discussion from Swapping Iron For Magnesium in the Ribosome:

An interesting question about this comes to mind. We know that the genetic code can evolve in living systems, so why don’t see see more than one cluster? I wonder if there are two things opposing drift too far from the universal code.

  1. The larger a genome gets, the harder it is to evolve the code, because it becomes harder impossible to adapt codons quickly enough.
  2. There are costs to becoming incompatible with the universal code, as now horizontal gene transfer will no longer be viable, except with compatible organisms.
  3. Larger more complex organisms are subject to 1. Bacteria are more subject to 2.

With that in mind, viruses are an interesting case. Changing the code could confer resistance to viruses. Viruses themselves seem constrained of the code of their host.

Archea is another interesting case. It is a different domain of life, but has the same code as bacteria, perhaps the compatibility is selected for because it enables horizontal gene transfer?

@Art, @mercer, @cwhenderson, @glipsnort (and the other biologists) has anyone thought about this? I wonder how we could test it…or if someone else did already. Is there a way to test for the selective positives and negatives of having an altered genetic code in different contexts?

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What you mean, presumably, is that there will be lots of sequences in which the translated amino acid will change, increasing the chance of a lethal or at least strongly disadvantageous result.

Is that actually a cost? It seems to require a very long-term and hypothetical benefit, not the sort of thing natural selection is capable of seeing. And there’s an immediate benefit: viruses from other species will lose the ability to infect the species.

The usual story is that changes in the code happen only to codons that occur so rarely in the genome that a change has little effect. The bigger the protein-coding genome, the less likely that a rare codon will be rare enough, i.e. won’t occur in a spot where a change would be strongly disadvantageous. On the other hand, with a small genome, a rare codon may randomly have zero representation from time to time.

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You get my logic precisely. I’m just wondering how and if it has been tested. Do you have references, or are you just arguing from basic logic?

I’d say it is an opportunity cost, which inhibits long term relative fitness. It is an example of long term selection for evolvability.

This might be a new take, which is not in the literature. The high frequency of horizontal gene transfer was less appreciated in the past, though it was certainly known to be real.

By “it” do you mean the selective cost of a variant code? If so, how would you test it? The benefits of horizontal transfer are something that could only be measured over millions or billions of generations, if at all. And it’s like asking whether the small size of most Cretaceous mammals was selected for its advantage in surviving the K/T extinction.

The problem with long term selection for evolvability is that it can’t credibly select, in the normal sense. It requires selection long before the selective event happens. It’s possible that species selection (or in this case, probably ordinal or class selection) might operate here. But of course that requires a species that’s already had a change in the code.

It seems to me that the distribution of alternate codes is most simply explained by the rarity of change in code due to the obvious selection against it rather than some hypothetical very long term disadvantage.

I don’t think anyone is in a position at present to weigh selective tradeoffs, beyond the kind of plausibility arguments already seen in this thread. Artificially recoded bacteria have been shown to be resistant to infection by standard phages, and naturally occurring recoded bacteria have been associated (via CRISPR spacers) with phages with the same recoding. But phages with a different recoding (recoding of amber, which has not been observed in prokaryotes) seem to be able to infect bacteria with the standard code; see here.

Am I wrong to think that viruses must have originally been a symbiotically advantageous way of sharing genetic information?

I think you are.

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There are many different types of viruses, and each might have a different sort of origin.

True, but it’s hard to credit that any of them have their origin as an evolved mechanism of sharing information.

@John_Harshman it is hard to discern the intrinsic purpose of anything.

In this context, it could mean “was the benefit of gene transfer one of the selective factors driving the origin of some viruses?”

I can easily imagine hypotheses that would answer “yes” in some cases.

I did quite a bit of reading about non-standard codes a while back and my overall impression was that most–and maybe all–cases (it is clearly an evolved conditions multiple times) the origins of the non-standard code could be best described to neutral processes rather than selection.They seem to be accidents that once fixed become required for future survival and thus maintained. Now there may be secondary benefits. Once the organism is using that secondary code they may find uses for it but those may have arisen opportunistically rather than the reason for the shift to a non-standard code.
RNA editing (e.g. C-U editing) may also be another accident or secondary effect of another phenomena


No disagreement there.

No worries. Asking stupid questions is a professional necessity for me. My knowledge of sciences is broad, but not very deep. I often need to ask and confirm my understanding before I can do an analysis correctly. Asking the stupid questions up front is better than not asking and getting it wrong (I’ve done that too).

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My point: it’s very hard to come up with credible scenarios in which evolvability evolves under selection (rather than as a byproduct for selection on something else or just neutrally), because anything that happens very seldom compared to the generation time of an individual can’t exert selection except at that very time, and if the time in between such events is long, there’s plenty of time for such features to be lost, either through selection or drift. Evolvability is one of those features that come in handy only on those long time scales. In order to be favored by selection, a trait must have frequent advantage.

Further, the only viruses around today that have much to do with gene exchange are retroviruses, which occasionally incorporate host DNA into their genomes and also occasionally integrate into host genomes. There are much simpler ways to do gene exchange, much more directly.

Thanks for the responses. I’ve bothered the Pros enough for one day, so I’ll save my next wild speculation for another time. :slight_smile:

I don’t buy this claim.

If there is a benefit to evolving a feature, the populations that acquire that benefit are capable of evolving that feature. Those that do not have that capability certainly do not evolve that feature. That alone grants an immediate benefit to evolvability, and speed of evolvability too.

Taking this further, recognizing that selective forces are often changing, populations that can evolve to adapt to these changes have a selective advantage.

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I think we differ on the frequency with which these “evolvability” advantage situations come up. Of course that depends on the particular “evolvability” feature we’re talking about. In the present case we’re talking about viruses, and I don’t see evolvability due to virus action being a very common occurrence. It might be, however, that willingness to take up foreign plasmids might fit your needs.

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I don’t think it is frequent. I do however think this dynamic is necessary to explain several features of life:

  1. Introns, exons, and spicing.

  2. The reverse complement ompimization of the genetic code.

  3. Plasmids, as you suggest, are a great example.

  4. The tetraploidy event at the root of vertebrates.

  5. Recombination, Mieosis, and sexual reproduction.

  6. Transposon based evolution.

I’m sure you could find other examples. These are all rare events, but they seem both individually and in aggregate as very important.

This is quite a disparate list. Some of them are potentially events by which evolvability might evolve, but others are just evolvability in action, and still others are just events that happened to result in evolutionary change. I don’t think anyone them happened with the selective “purpose” of increasing evolvability, though a few of them had that result.

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What do you mean by purpose? That is a squish word.

I’m rather saying that the first individuals to claim the selective benefit of a beneficial mutation are more likely to be more evolvable than their neighbors. So selection for new/improved function intrinsically selects for evolvability. That is quite a list, because all those things make it easier to evolve a beneficial mutation, and more likely therefore to end up selected.

I would agree that the much of this process might be neutral initially. However, it causes the beneficial mutations that contribute its selection. So we can’t quite call it neutral draft. There is a causative relationship between evolvability and selection.