Testing the covarion hypothesis of molecular evolution.
Testing the covarion hypothesis of molecular evolution.
复制标题
检验分子进化的协变假说。
DOI：
10.1093/oxfordjournals.molbev.a040224
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发表时间：
1995
影响因子：
10.7
通讯作者：
Fitch,WM
中科院分区：
文献类型：
--
作者：
Miyamoto,MM;Fitch,WM
分子进化的协变假设指出，突变的固定可能会改变任何给定位置修复下一次变化的概率。使用真实序列的发散度对这一假设的测试受到损害，因为位置之间的速率变化模型(例如，单参数方程的伽马版本)预测的序列发散值类似于协方差过程的发散值。因此，这项研究的重点是两个差异很大的分类群的不同密码子和不变密码子的相同程度，因为协变异体假说预期的密码子比伽马模型所预期的要少。这些测试的数据是哺乳动物和植物的铜锌超氧化物歧化酶(SOD)的蛋白质序列。模拟分析表明，协方差假设对这两个分类群之间共同的不同和未命中位置的频率做出了更好的预测，而不是伽马版本的单参数模型。此外，对SOD三级结构的分析表明，哺乳动物和植物的变异体在蛋白质上的分布是不同的。这些结果支持这样的结论，即哺乳动物和植物Sod的可变和不变密码子是不同的，协变模型比单参数过程的Gamma版本更好地解释了该蛋白质的进化。与其他模型不同的是，协变量假说解释了位置之间的速率随时间的波动，这是分子进化的一个重要参数。
The covarion hypothesis of molecular evolution states that the fixation of mutations may alter the probability that any given position will fix the next change. Tests of this hypothesis using the divergence of real sequences are compromised because models of rate variation among sites (e.g., the gamma version of the one-parameter equation) predict sequence divergence values similar to those for the covarion process. This study therefore focuses on the extent to which the varied and unvaried codons of two well-diverged taxa are the same, because fewer are expected by the covarion hypothesis than by the gamma model. The data for these tests are the protein sequences of Cu, Zn superoxide dismutase (SOD) for mammals and plants. Simulation analyses show that the covarion hypothesis makes better predictions about the frequencies of varied and unhit positions in common between these two taxa than does the gamma version of the one-parameter model. Furthermore, the analysis of SOD tertiary structure demonstrates that mammal and plant variabilities are distributed differently on the protein. These results support the conclusions that the variable and invariable codons of mammal and plant SODs are different and that the covarion model explains the evolution of this protein better than the gamma version of the one-parameter process. Unlike other models, the covarion hypothesis accounts for rate fluctuations among positions over time, which is an important parameter of molecular evolution.