The power of relative rates tests depends on the data
The power of relative rates tests depends on the data
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DOI：
10.1007/s002399910034
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发表时间：
2000-03-01
影响因子：
3.9
通讯作者：
Hendy, MD
中科院分区：
文献类型：
--
作者：
Bromham, L;Penny, D;Hendy, MD
分子系统发育分析最有用的特征之一是从现存物种的DNA中估计进化谱系分歧的日期。但是，分子进化速率的谱系特异性变化使分子定年复杂化，因为从一个谱系估计的校准速率可能不能准确地代表其他谱系的速率。许多分子测年研究使用“时钟测试”来识别和排除不同谱系之间速率不同的序列。然而，这些时钟测试不应该依赖于没有严格审查其有效性，从任何给定的数据集，特别是在删除速率可变序列的序列长度和可变位点的数量。作为这个问题的一个例子，我们提出了一个经常采用的三重相对速率测试的功率测试。我们的结论是：（1）相对速率检验不太可能检测到中等水平的谱系特异性速率变化（其中一个谱系的分子进化速率是另一个的1.5至4.0倍），对于分子测年分析中最常用的序列，（2）这种缺乏效力的情况可能导致在估计分歧日期时出现重大错误。作为一个例子，我们研究表明，鼠啮齿类动物和类人猿之间的差异率将不会被检测到的许多序列用于日期之间的分歧，这两个谱系，这种未能检测到率的变化很可能会导致一致高估的啮齿类灵长类动物分裂。
One of the most useful features of molecular phylogenetic analyses is the potential for estimating dates of divergence of evolutionary lineages from the DNA of extant species. But lineage-specific variation in rate of molecular evolution complicates molecular dating, because a calibration rate estimated from one lineage may not be an accurate representation of the rate in other lineages. Many molecular dating studies use a "clock test" to identify and exclude sequences that vary in rate between lineages. However, these clock tests should not be relied upon without a critical examination of their effectiveness at removing rate variable sequences from any given data set, particularly with regard to the sequence length and number of variable sites. As an illustration of this problem we present a power test of a frequently employed triplet relative rates test. We conclude that (1) relative rates tests are unlikely to detect moderate levels of lineage-specific rate variation (where one lineage has a rate of molecular evolution 1.5 to 4.0 times the other) for most commonly used sequences in molecular dating analyses, and (2) this lack of power is likely to result in substantial error in the estimation of dates of divergence. As an example, we show that the well-studied rate difference between murid rodents and great apes will not be detected for many of the sequences used to date the divergence between these two lineages and that this failure to detect rate variation is likely to result in consistent overestimation the elate of the rodent-primate split.