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Genetic codes as evolutionary filters: subtle differences in the structure of genetic codes result in significant differences in patterns of nucleotide substitution

机译:遗传密码作为进化过滤器:遗传密码结构的细微差异导致核苷酸取代方式的重大差异

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摘要

The codon-degeneracy model (CDM) predicts that patterns of nucleotide substitution in protein-coding genes are largely determined by the relative frequencies of four-fold (40, two-fold, and non-degenerate sites, the attributes of which are determined by the structure of the governing genetic code. The CDM thus further predicts that genetic codes with alternative structures will "filter" molecular evolution differentially. A method, therefore, is presented by which the CDM may be applied to the unique structure of any genetic code. The mathematical relationship between the proportion of transitions at 4f degenerate nucleotide sites and the transition-to-transversion ratio is described. Predictions for five individual genetic codes, relative to the relationship between code structure and expected patterns of nucleotide substitution, are clearly defined. To test this "filter" hypothesis of genetic codes, simulated DNA sequence data sets were generated with a variety of input parameter values to estimate the relationship between patterns of nucleotide substitution and best-fit estimates of transition bias at 4f degenerate sites for both the universal genetic code and the vertebrate mitochondrial genetic code. These analyses confirm the prediction of the CDM that, all else being equal, even small differences in the structure of alternative genetic codes may result in significant shifts in the overall pattern of nucleotide substitution. (C) 2003 Elsevier Ltd. All rights reserved.
机译:密码子简并模型(CDM)预测蛋白质编码基因中核苷酸取代的模式主要由四倍(40,两倍和非简并位点)的相对频率决定,其相对位置由因此,CDM进一步预测具有替代结构的遗传密码将差异地“过滤”分子进化,因此,提出了一种方法,通过该方法,CDM可以应用于任何遗传密码的独特结构。描述了在4f简并核苷酸位点上的过渡比例与过渡与转化率之间的数学关系,并明确定义了五个独立遗传密码的预测,相对于密码结构与核苷酸取代的预期模式之间的关系。测试此“过滤器”遗传密码假设,使用各种输入参数val生成模拟的DNA序列数据集我们需要评估通用遗传密码和脊椎动物线粒体遗传密码在4f简并位点的核苷酸取代模式与过渡偏倚的最佳拟合估计之间的关系。这些分析证实了CDM的预测,即在所有其他条件相同的情况下,即使替代遗传密码的结构存在很小差异,也可能导致核苷酸取代整体模式的重大转变。 (C)2003 Elsevier Ltd.保留所有权利。

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