一种基于协变子的分子适应性检测方法：应用于灵长类动物线粒体基因组的进化研究
A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes.
作者信息
Pupko Tal, Galtier Nicolas
机构信息
The Institute of Statistical Mathematics, 4-6-7 Minami-Azabu Minato-ku, Tokyo 106-8569, Japan.
出版信息
Proc Biol Sci. 2002 Jul 7;269(1498):1313-6. doi: 10.1098/rspb.2002.2025.
Abstract
A new method for detecting site-specific variation of evolutionary rate (the so-called covarion process) from protein sequence data is proposed. It involves comparing the maximum-likelihood estimates of the replacement rate of an amino acid site in distinct subtrees of a large tree. This approach allows detection of covarion at the gene or the amino acid levels. The method is applied to mammalian-mitochondrial-protein sequences. Significant covarion-like evolution is found in the (simian) primate lineage: some amino acid positions are fast-evolving (i.e. unconstrained) in non-primate mammals but slow-evolving (i.e. highly constrained) in primates, and some show the opposite pattern. Our results indicate that the mitochondrial genome of primates reached a new peak of the adaptive landscape through positive selection.
摘要
提出了一种从蛋白质序列数据中检测进化速率位点特异性变异（即所谓的共变过程）的新方法。该方法涉及比较大树不同子树中氨基酸位点替换率的最大似然估计值。这种方法能够在基因或氨基酸水平上检测共变。该方法应用于哺乳动物线粒体蛋白质序列。在（猿猴）灵长类谱系中发现了显著的类似共变的进化现象：一些氨基酸位置在非灵长类哺乳动物中进化迅速（即不受约束），而在灵长类动物中进化缓慢（即高度受限），还有一些则呈现相反的模式。我们的结果表明，灵长类动物的线粒体基因组通过正选择达到了适应景观的一个新高峰。
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本文引用的文献
1
Positive and negative selection on the human genome.人类基因组的正向和负向选择
Genetics. 2001 Jul;158(3):1227-34. doi: 10.1093/genetics/158.3.1227.
2
Maximum-likelihood phylogenetic analysis under a covarion-like model.在类可变位点模型下的最大似然系统发育分析。
Mol Biol Evol. 2001 May;18(5):866-73. doi: 10.1093/oxfordjournals.molbev.a003868.
3
Molecular phylogenetics and the origins of placental mammals.分子系统发育学与胎盘哺乳动物的起源
Nature. 2001 Feb 1;409(6820):614-8. doi: 10.1038/35054550.
4
Parallel adaptive radiations in two major clades of placental mammals.胎盘哺乳动物两个主要分支中的平行适应性辐射。
Nature. 2001 Feb 1;409(6820):610-4. doi: 10.1038/35054544.
5
Interordinal relationships and timescale of eutherian evolution as inferred from mitochondrial genome data.从线粒体基因组数据推断的真兽类进化的目间关系和时间尺度。
Gene. 2000 Dec 23;259(1-2):149-58. doi: 10.1016/s0378-1119(00)00427-3.
6
Molecular evolution of aerobic energy metabolism in primates.灵长类动物有氧能量代谢的分子进化
Mol Phylogenet Evol. 2001 Jan;18(1):26-36. doi: 10.1006/mpev.2000.0890.
7
Evolutionary rate acceleration of cytochrome c oxidase subunit I in simian primates.猿猴灵长类动物细胞色素c氧化酶亚基I的进化速率加速
J Mol Evol. 2000 Jun;50(6):562-8. doi: 10.1007/s002390010059.
8
Where do rodents fit? Evidence from the complete mitochondrial genome of Sciurus vulgaris.松鼠在其中处于什么位置？来自普通松鼠完整线粒体基因组的证据。
Mol Biol Evol. 2000 Jun;17(6):979-83. doi: 10.1093/oxfordjournals.molbev.a026379.
9
Rapid evolution of male reproductive genes in the descent of man.人类进化过程中男性生殖基因的快速演变。
Nature. 2000 Jan 20;403(6767):304-9. doi: 10.1038/35002070.
10
The root of the tree of life in the light of the covarion model.基于协变模型的生命之树根源
J Mol Evol. 1999 Oct;49(4):496-508. doi: 10.1007/pl00006572.
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