Estimating divergence times in the presence of an overdispersed molecular clock
Estimating divergence times in the presence of an overdispersed molecular clock
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DOI：
10.1093/oxfordjournals.molbev.a026264
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发表时间：
2000-11-01
影响因子：
10.7
通讯作者：
Cutler, DJ
中科院分区：
文献类型：
--
作者：
Cutler, DJ
未通过相对速率检验的分子基因座被称为“过度分散的”。传统的用于估计分化时间的分子钟方法没有考虑到这一点。在这项研究中，开发了一种方法，用于使用可能过度分散的基因座来估计分化时间。该方法是用更普遍的平稳过程假设取代传统的泊松过程假设。建立了一个概率模型，并编写了一个配套的计算机程序，以便在泊松过程和平稳过程假设下找到分化时间的最大似然估计值。在模拟中，表明传统泊松假设下的置信区间往往大大低估了过度分散基因座的真实置信限。两种模型都应用于两个数据集：一个来自陆生植物，另一个来自高等后生动物。在这两种情况下，传统的泊松过程模型都可以被高度确信地拒绝。在更普遍的平稳过程下对后生动物数据集进行的最大似然分析表明，它们的辐射发生在十亿多年前，但置信区间极宽。还表明，一个与动物门的寒武纪（或接近寒武纪）起源相符的模型，尽管比更古老的分化可能性显著更低，但也能很好地拟合数据。有人认为，如果没有对替换之间时间方差的先验了解，分子数据集可能永远无法确定后生动物辐射的年龄。
Molecular loci that fail relative-rate tests are said to be "overdispersed." Traditional molecular-clock approaches to estimating divergence times do not take this into account. In this study, a method was developed to estimate divergence times using loci that may be overdispersed. The approach was to replace the traditional Poisson process assumption with a more general stationary process assumption. A probability model was developed, and an accompanying computer program was written to find maximum-likelihood estimates of divergence times under both the Poisson process and the stationary process assumptions. In simulation, it was shown that confidence intervals under the traditional Poisson assumptions often vastly underestimate the true confidence limits for overdispersed loci. Both models were applied to two data sets: one from land plants, the other from the higher metazoans. In both cases, the traditional Poisson process model could be rejected with high confidence. Maximum-likelihood analysis of the metazoan data set under the more general stationary process suggested that their radiation occurred well over a billion years ago, but confidence intervals were extremely wide. It was also shown that a model consistent with a Cambrian (or nearly Cambrian) origination of the animal phyla, although significantly less likely than a much older divergence, fined the data well. It is argued that without an a priori understanding of the variance in the time between substitutions, molecular data sets may be incapable of ever establishing the age of the metazoan radiation.