Mutation bias reflects natural selection in Arabidopsis thaliana

I take this to mean that DNA repair mechanisms are more active in sensitive critical regions, and less active where potentially beneficial mutations can be tolerated?


Yes it seems to be in some sense the reverse of somatic hypermutation. Rather than have particular regions targeted for high rates of mutation by enzymes that make mutations occur, some genomic regions are instead much more protected against mutation by different protective mechanisms.

Of course the finding that mutations are not distributed with equal probability across the genome as a whole, and that there are mutational hot spots and cold spots, has been known for a long time now.
Does a bias in a probability distribution make the process non-random? Mutations still appear to occur everywhere, just with unequal frequency, so in some places more than others. And in places with critical and house-keeping genes they’re more protected.

That doesn’t seem to me to substantiate any claim that mutations are directed to be more adaptive(as if the organism knows what kinds of mutations will be adaptive), since the organism can’t know whether mutations in a house-keeping gene might turn out to be adaptive in some future circumstance. This biasing of mutations to be lower in some regions is analogous to an adaptive, but ultimately still probabilistic behavioral strategy. Act in a certain way because this has in the past, on average, been less likely to be detrimental.

So no, I don’t think this is actually “challenging the prevailing paradigm that mutation is a directionless force in evolution.” It looks like textbook evolutionary game-theory, but with mutation biases instead of behavior.


Somatic hypermutation is not that particular wrt mutagenesis itself. The complexity of it shows how evolution cobbled it together. Mutation is selectively increased in highly expressed genes (transcription is literally required) in general, but mutations are not being repaired as often in the immunoglobulin genes. Thus the latter is a refinement layered upon the former, which still had adaptive value on its own. That’s still an oversimplification, because IIRC only one of the two major repair pathways is dialed down.

Exactly. They’ve never been alleged to be random in any other way, except by creationists looking to pummel a straw man.


Did you mean decreased?

No, I mean increased. I’m talking about somatic hypermutation in B-cell maturation. It’s one of the main reasons why we can get boosters of the same COVID vaccine that manage to increase our immunity to variants. The larger point that @Rumraket was making is that mutation rates can be dialed up as well as down.


A stupid-statistician question. It’s a professional hazard. :exploding_head:

Not stupid at all, thanks for asking.

I see so many different topic that I sometimes need to ask very simple questions to confirm my understanding. Sometimes it goes the other way - once asked if sex was an important analysis variable on a survey of pregnant teenagers. Doh!


Some questions about this study have been raised:

The abstract:

A study of the plant Arabidopsis thaliana detected lower mutation rates in genomic regions where mutations are more likely to be deleterious, challenging the principle that mutagenesis is blind to its consequence. To examine the generality of this finding, we analyze large mutational data from baker’s yeast and humans. The yeast data do not exhibit this trend, whereas the human data show an opposite trend that disappears upon the control of potential confounders. We find that the Arabidopsis study identified substantially more mutations than reported in the original data-generating studies and expected from Arabidopsis’ mutation rate. These extra mutations are enriched in polynucleotide tracts and have relatively low sequencing qualities so are likely sequencing errors. Furthermore, the polynucleotide “mutations” can produce the purported mutational trend in Arabidopsis. Together, our results do not support lower mutagenesis of genomic regions of stronger selective constraints in the plant, fungal, and animal models examined.


The abstract:

It has recently been proposed that lower mutation rates in gene bodies compared with upstream and downstream sequences in Arabidopsis thaliana are the result of an “adaptive” modification of the rate of beneficial and deleterious mutations in these functional regions. This claim was based both on analyses of mutation accumulation lines and on population genomics data. Here, we show that several questionable assumptions were used in the population genomics analyses. In particular, we demonstrate that the difference between gene bodies and less selectively constrained sequences in the magnitude of Tajima’s D can in principle be explained by the presence of sites subject to purifying selection and does not require lower mutation rates in regions experiencing selective constraints.


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