Intuitively, once you have the idea that some DNA is responsible for turning on and off the DNA that codes for proteins, it's possible to imagine that the regulatory DNA is actually the most important part. In the ingredients list of a recipe, you might think the coding DNA gives you the list of ingredients, but the regulatory DNA gives you the amounts of each one, plus the order in which you add them to the bowl. If that's true, then different variants of regulatory DNA should be selected for and against, and evolutionary molecular biologists ought to be tracking those variants like they track alleles of genes. But evolution always is discussed as if it's just about different gene frequencies.

Is "regulatory evolution" a thing? If so, is there an understanding of how big a thing it is? Or, if not, why not?

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    $\begingroup$ Evolution is rarely about gene frequencies — much research does, however, focus on allele frequencies. In any case, in a modern context a gene includes its regulatory sequences. While allelic differences resulting from changes in regulatory sequences are harder to identify they most certainly are being considered, so I'm afraid your question is based on a false assumptions about both genes and evolution! $\endgroup$
    – tyersome
    Mar 9 at 6:41
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    $\begingroup$ I think the focus on gene/allele frequencies is more due to the historical reasons - notion of gene is rather old, preceding even the knowledge about the DNA, whereas the existence of regulatory DNA is recent knowledge. However, most of the discussions about genes/alleles are easily transposed to the regulatory DNA. I agree with @tyersome that gene and allele are not the same thing... but these words are used interchangeably in many contexts. $\endgroup$ Mar 9 at 7:18

Yes, a simple google search reveals millions of academic citations talking about "regulatory evolution".

But it's a little over-simplistic to divide coding vs. regulatory DNA. Indeed, some coding DNA is in fact also regulatory at the level of determining gene expression in cis (a well-known example of this would be codon usage).

It is moreover incorrect to think that coding DNA products don't do gene regulation. This was recognized very early on in the ideas of "structural gene" vs. "regulatory gene". These days we would call the latter transcription factors, we don't really use the structural/regulatory terminology anymore. Transcription factors do most of the actual active work of gene regulation in trans, in collaboration of course with regulatory DNA.

So in conclusion, yes it's important and there are tons of studies that you can google if you want to investigate these problems. I would suggest reading more about cis-regulatory and trans-regulatory elements. Of course, there isn't an exact mapping of coding<-->trans and noncoding<-->cis, it's just a helpful simplification.


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