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DOI | 10.1371/journal.pgen.0030147 |
Adaptive evolution of conserved noncoding elements in mammals | |
Kim, Su Yeon; Pritchard, Jonathan K. | |
通讯作者 | Kim, Su Yeon |
来源期刊 | PLOS GENETICS |
ISSN | 1553-7390 |
出版年 | 2007 |
卷号 | 3期号:9页码:1572-1586 |
英文摘要 | 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; similar to 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; similar to 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. |
类型 | Article |
语种 | 英语 |
国家 | USA |
收录类别 | SCI-E |
WOS记录号 | WOS:000249767800002 |
WOS关键词 | MUTATION-RATE VARIATION ; HUMAN GENOME ; NONGENIC SEQUENCES ; MAXIMUM-LIKELIHOOD ; CHICKEN GENOME ; GENE DESERTS ; HUMANS ; IDENTIFICATION ; VERTEBRATE ; REGIONS |
WOS类目 | Genetics & Heredity |
WOS研究方向 | Genetics & Heredity |
资源类型 | 期刊论文 |
条目标识符 | http://119.78.100.177/qdio/handle/2XILL650/155725 |
作者单位 | (1)Univ Chicago, Dept Stat, Chicago, IL 60637 USA;(2)Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA |
推荐引用方式 GB/T 7714 | Kim, Su Yeon,Pritchard, Jonathan K.. Adaptive evolution of conserved noncoding elements in mammals[J],2007,3(9):1572-1586. |
APA | Kim, Su Yeon,&Pritchard, Jonathan K..(2007).Adaptive evolution of conserved noncoding elements in mammals.PLOS GENETICS,3(9),1572-1586. |
MLA | Kim, Su Yeon,et al."Adaptive evolution of conserved noncoding elements in mammals".PLOS GENETICS 3.9(2007):1572-1586. |
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