What's the explanation for Ultra-Conserved Elements?

Cornelius Hunter says that Ultra-Conserved Elements are a problem for evolution. I don’t know enough about genetics to answer this, so I’m posting it here. Could someone explain to me how UCE fit with the notion that most of our DNA is non-functional?

It fits simply through the fact that most DNA isn’t ultra-conserved. Though we would expect a general correlation between conservation and function, there are possible and interesting edge cases that lie outside those expectations. We cannot say, for example, that just because a sequence isn’t conserved, that this makes it a logical necessity that it has no function. After all, it is possible it only recently evolved to acquire a function in a single species, after the split from the most recent common ancestor. So in this case sequence conservation would imply the locus is nonfunctional, yet it is not. There are possible mechanistic explanations for why actual junk without a function could nevertheless also be conserved through byproducts of selection on other factors/processes.

Most DNA (at least in the human genome) is basically evolving at the rate of mutation, so not at all conserved and is diverging at the rate expected of DNA that either has no function at all (therefore almost all mutations will be tolerated), or alternatively if some of it does have some function then that function is almost completely independent of sequence.
With respect to sequence-independent functions, think of “spacer” or “bulk” DNA functions that just sits there to produce a certain amount of distance between other loci that do have sequence-dependent functions such as coding for a particular protein’s amino acid sequence.

So there is just no logical contradiction implied between the two statements:
A) Most DNA is nonfunctional junk.
B) Some pieces of DNA are ultra-conserved.

With respect to Cornelius Hunter’s anonymous friend’s opinions on the possibility of falsification of evolution, I think there’s a reason he’s anonymous. The possibility that some ultraconserved elements couldn’t possibly be functionless just isn’t and never was a prediction of evolution. He’s just making stuff up. It also betrays a simplistic and overly dichotomous view of science as some sort of naive, black-and-white falsificationism. The real world just is a lot more complicated than this, and science progresses in large part by competing model fitting and statistical testing.

It gets even worse when we try to make sense of what Hunter is suggesting in place of evolution. Isn’t he saying, essentially, that these elements are conserved because they’re somehow teleologically “intending” to remain conserved? How does this square with the apparent experimental results that their removal have no phenotypic effects, and how do they mechanistically accomplish their conservation anyway? Magic? Never mind the problems he mistakenly thinks these elements constitute for evolution, he can make no sense of them at all on design. They’re just there for no apparent historical or functional reason and they just remain conserved because, well, they want to? ROFL.


That’s simple enough. Some of our DNA isn’t non-functional, and UCEs belong to that fraction. We may not know just what they do, but they must do something that critically depends on their exact sequences. Not sure why anyone would consider that a paradox.

I notice that Hunter doesn’t mention how ID predicts UCEs and what in ID accounts for their conservation. Why do you suppose that is?


Yeah I think it’s important to remember that even a relatively small reduction in fitness due to mutation that wouldn’t be directly visible as a developmental or behavioral effect, can still be enough to conserve these elements on evolutionary timescales. Evolutionary pressures can manifest so weakly, or under conditions where they’re not really visible under laboratory conditions. All of this is discussed in the actual paper.

Meanwhile, Hunter says, basically, that we haven’t yet figured out what it does therefore evolution is untestable.

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One thing I would add - given a stretch of non- functional DNA that is evolving randomly, it is inevitable that some stretches of sequence will have fewer (even no) variants while other regions will have many changes. “Random” does not mean “uniform”.

So there is no reason to jump up and down about some stretches of hundreds of bp of “junk DNA” that are highly conserved between mice and humans. And certainly no reason to claim that their existence in some way is a death knell for evolution.

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We’re talking about hundreds of bases (by definition, >200) that are invariant throughout amniotes, at a minimum, not just humans and mice. This can’t possibly be due to chance. Conservation over such a broad range of taxa over hundreds of millions of years — that’s billions of years of independent lineage evolution — is more improbable than you suppose here. UCEs must either be conserved by selection or by some unknown (and unlikely) additional mechanism. I vote for selection, which as @Rumraket mentioned, need not be very strong, just constantly in effect.

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The first sentence of the abstract of the paper Hunter et al. are talking about:

Across the human genome, there are nearly 500 ‘ultraconserved’ elements: regions of at least 200 contiguous nucleotides that are perfectly conserved in both the mouse and rat genomes.

I would maintain that selection is not needed to explain these sorts of ultraconserved elements.

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Possibly, if the sample were only of Homo sapiens, Mus musculus, and Rattus rattus. But the conservation is over a much broader range than that. And even given that restricted definition, have you tried computing the probability of finding even one such sequence by chance in a genome, given a reasonable neutral rate? We’re talking about hundreds of millions of years of total lineage evolution here.

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Then how would you explain them? Why have they remain unchanged for hundreds of millions of years if not by purifying selection?

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“What’s the explanation for ultra-conserved elements?”

Right-wing talk radio.