Wednesday, July 18, 2007

New Pritchard paper, Adaptive evolution of conserved non-coding elements in mammals   posted by Razib @ 7/18/2007 10:10:00 AM

Jonathan Pritchard has a new provisional paper, Adaptive evolution of conserved non-coding elements in mammals, in PLOS Genetics:
Conserved non-coding 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' (SRT) 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.

Interestingly, there another paper another paper out in PNAS which speaks to the possibility of non-coding genomic regions in humans having functional significance.