A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome.
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome.
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DOI：
10.1093/oxfordjournals.molbev.a040152
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发表时间：
1994-09
影响因子：
10.7
通讯作者：
S. Muse;B. Gaut
中科院分区：
文献类型：
--
作者：
S. Muse;B. Gaut
提出了一个适用于编码区的DNA序列进化模型。这代表了第一个解释密码子内核苷酸之间依赖性的进化模型。该模型使用密码子，而不是核苷酸，作为进化的单位，并在同义和非同义核苷酸取代率方面进行参数化。该模型的优点之一，在那些用于估计同义和非同义取代率的方法中使用的是，它完全纠正多个命中在一个密码子，而不是采取简约的方法，并考虑同源密码子之间的最小变化的途径。似然比版本的相对速率测试的构建和应用的数据从水稻，烟草，地钱多形叶绿体DNA序列。这些测试的结果证实了先前的研究结果，即叶绿体基因组中的取代率受到谱系特异性和基因座特异性的影响。此外，新的测试表明，率异质性主要是由于非同义替换率的差异。模拟有助于确认以前的建议，沉默的网站是饱和的，没有留下任何证据的异质性同义替换率。
A model of DNA sequence evolution applicable to coding regions is presented. This represents the first evolutionary model that accounts for dependencies among nucleotides within a codon. The model uses the codon, as opposed to the nucleotide, as the unit of evolution, and is parameterized in terms of synonymous and nonsynonymous nucleotide substitution rates. One of the model's advantages over those used in methods for estimating synonymous and nonsynonymous substitution rates is that it completely corrects for multiple hits at a codon, rather than taking a parsimony approach and considering only pathways of minimum change between homologous codons. Likelihood-ratio versions of the relative-rate test are constructed and applied to data from the complete chloroplast DNA sequences of Oryza sativa, Nicotiana tabacum, and Marchantia polymorpha. Results of these tests confirm previous findings that substitution rates in the chloroplast genome are subject to both lineage-specific and locus-specific effects. Additionally, the new tests suggest tha the rate heterogeneity is due primarily to differences in nonsynonymous substitution rates. Simulations help confirm previous suggestions that silent sites are saturated, leaving no evidence of heterogeneity in synonymous substitution rates.