Reliable Confidence Intervals for RelTime Estimates of Evolutionary Divergence Times
Reliable Confidence Intervals for RelTime Estimates of Evolutionary Divergence Times
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DOI：
10.1093/molbev/msz236
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发表时间：
2020-01-01
影响因子：
10.7
通讯作者：
Kumar, Sudhir
中科院分区：
文献类型：
--
作者：
Tao, Qiqing;Tamura, Koichiro;Kumar, Sudhir
置信区间（CI）描述了进化发散时间估计的统计不确定性。它们捕获由比对中使用的有限数量的序列和位点、进化速率与同源性中严格的分子钟的偏差以及与时钟校准相关的不确定性所贡献的方差。生物学假设的可靠检验需要可靠的CI。然而，目前的非贝叶斯方法可能会产生不可靠的CI，因为它们没有适当地纳入谱系之间的速率变化和时钟校准之间的相互作用。在这里，我们提出了一种新的分析方法来计算使用RelTime方法估计的发散时间的CI，沿着的方法，利用多个校准不确定性密度的定年分析。经验数据分析表明，新方法产生的CI与贝叶斯最高后验密度区间重叠。在对计算机模拟数据的分析中，我们发现RelTime CI显示出出色的平均覆盖概率，即实际时间以94%的概率包含在CI内。这些发展将鼓励在分子测年分析和生物学假设检验中更广泛地使用计算效率高的RelTime方法。
Confidence intervals (CIs) depict the statistical uncertainty surrounding evolutionary divergence time estimates. They capture variance contributed by the finite number of sequences and sites used in the alignment, deviations of evolutionary rates from a strict molecular clock in a phylogeny, and uncertainty associated with clock calibrations. Reliable tests of biological hypotheses demand reliable CIs. However, current non-Bayesian methods may produce unreliable CIs because they do not incorporate rate variation among lineages and interactions among clock calibrations properly. Here, we present a new analytical method to calculate CIs of divergence times estimated using the RelTime method, along with an approach to utilize multiple calibration uncertainty densities in dating analyses. Empirical data analyses showed that the new methods produce CIs that overlap with Bayesian highest posterior density intervals. In the analysis of computer-simulated data, we found that RelTime CIs show excellent average coverage probabilities, that is, the actual time is contained within the CIs with a 94% probability. These developments will encourage broader use of computationally efficient RelTime approaches in molecular dating analyses and biological hypothesis testing.