Adaptive Evolution of Conserved Noncoding Elements in Mammals

 
"Adaptive Evolution of Conserved Noncoding Elements in Mammals" is the title of a paper that's just been published in PLoS Genetics [Kim and Pritchard (2007)].

With a title like that you'd think the paper would be really interesting because conserved noncoding elements are a hot topic. Recall that these are short sequences in the genomes of diverse mammals that are highly similar. They were thought to be examples of regulatory sequences but deleting them from the mouse genome seems to have no effect [The Role of Ultraconserved Non-Coding Elements in Mammalian Genomes]. It's a little puzzling to see "adaptive evolution" in the title since the very fact that these short sequences are conserved implies adaptation.

I took a look at the paper. Here's the abstract.

Conserved noncoding elements (CNCs) are an abundant feature of vertebrate genomes. Some CNCs have been shown to act as cis-regulatory modules, but the function of most CNCs remains unclear. To study the evolution of CNCs, we have developed a statistical method called the “shared rates test” to identify CNCs that show significant variation in substitution rates across branches of a phylogenetic tree. We report an application of this method to alignments of 98,910 CNCs from the human, chimpanzee, dog, mouse, and rat genomes. We find that ∼68% of CNCs evolve according to a null model where, for each CNC, a single parameter models the level of constraint acting throughout the phylogeny linking these five species. The remaining ∼32% of CNCs show departures from the basic model including speed-ups and slow-downs on particular branches and occasionally multiple rate changes on different branches. We find that a subset of the significant CNCs have evolved significantly faster than the local neutral rate on a particular branch, providing strong evidence for adaptive evolution in these CNCs. The distribution of these signals on the phylogeny suggests that adaptive evolution of CNCs occurs in occasional short bursts of evolution. Our analyses suggest a large set of promising targets for future functional studies of adaptation.

Okay. It's confusing but what they seem to be saying is that the sequences of these conserved noncoding elements change in various lineages. A lot of them seem to be evolving at a "neutral rate"—which raises the question of why they are "conserved" in the first place. Does it mean that the ancestor to all mammals had a functional sequence but that function has been lost? Some of these conserved elements evolve at a very rapid rate in some lineages and this is taken to be evidence of adaptive evolution in that lineage.

I read the entire paper. It's pretty much Greek to me. If anyone else can figure it out please feel free to post an explanation in the comments.