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• W2000499087 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." @default.
• W2000499087 created "2016-06-24" @default.
• W2000499087 creator A5030341663 @default.
• W2000499087 creator A5051388103 @default.
• W2000499087 date "2007-09-07" @default.
• W2000499087 modified "2023-10-16" @default.
• W2000499087 title "Adaptive Evolution of Conserved Noncoding Elements in Mammals" @default.
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• W2000499087 doi "https://doi.org/10.1371/journal.pgen.0030147" @default.
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• W2000499087 hasPublicationYear "2007" @default.
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