The codon-degeneracy model of molecular evolution
The codon-degeneracy model of molecular evolution
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DOI：
10.1007/s002399910015
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发表时间：
2000-02-01
影响因子：
3.9
通讯作者：
McClellan, DA
中科院分区：
文献类型：
--
作者：
McClellan, DA
线粒体遗传密码子可以根据第一密码子位置处的两倍或非简并位点和第三密码子位置处的两倍或四倍简并位点的不同组合通过核苷酸位点简并性的四种模式来分类。在此，引入了一个分子进化模型，该模型使用这些模式来计算每个密码子位置和取代类型相对于同义或非同义取代总数的预期取代频率。口袋地鼠细胞色素氧化酶亚基I（COI）和细胞色素B（cyt-B）基因的区域进行了分析，使用该模型。卡方分布用于产生相对拟合优度（GF）得分，用于测量由密码子简并模型（CDM）预测的取代频率与使用密切相关物种的良好支持的系统发育树推断的频率之间的差异。预期和观察到的同义（GF（syn）= 0.429，p = 0.807）和非同义（GF（ns）2.309，p = 0.679）取代频率的GF评分导致未能拒绝CDM作为囊地鼠中COI和cyt-b分子进化的零假设。这些数据的替代树拓扑结构和过渡偏差的计算导致更高的GF分数。
Mitochondrial genetic codons can be categorized by four patterns of nucleotide-site degeneracy based on varying combinations of twofold- or nondegenerate sites at first codon positions and twofold- or fourfold-degenerate sites at third codon positions. Herein, a model of molecular evolution is introduced that uses these patterns to calculate expected substitution frequencies for each codon position and substitution type relative to overall number of synonymous or nonsynonymous substitutions. Regions of the pocket gopher cytochrome oxidase subunit I (COI) and cytochrome b (cyt-b) genes are analyzed using this model. Chi-square distributions are used to produce relative goodness-of-fit (GF) scores for measuring the difference between substitution frequencies predicted by the codon-degeneracy model (CDM), and frequencies inferred using a well-supported phylogenetic tree of closely related species. The GF scores for expected and observed synonymous (GF(syn) = 0.429, p = 0.807) and nonsynonymous (GF(ns) 2.309, p = 0.679) substitution frequencies resulted in a failure to reject the CDM as a null hypothesis for the molecular evolution of COI and cyt-b in pocket gophers. Alternative tree topologies and calculations of transition bias for these data result in higher GF scores.