Data from: The local-clock permutation test: a simple test to compare rates of molecular evolution on phylogenetic trees

Rates of molecular evolution vary substantially between lineages, and a growing research effort is directed at uncovering the causes and consequences of this variation. Comparing local-clocks (rates of molecular evolution estimated from sets of branches of a phylogenetic tree) is a common tool in this research effort. Here, I show that a commonly used test (the Likelihood Ratio Test, LRT) will not be statistically valid for comparing local-clocks in most cases. Instead, I propose the local-clock permutation test (LCPT), a simple test which can be used to test the significance of differences between local-clocks. The LCPT could also be used to test for differences between any parameter that can be assigned to individual branches on a phylogenetic tree. Using simulated data, I show that the LCPT has good power to detect differences between local-clocks.

不同演化支间的分子进化速率差异显著，当前越来越多的研究致力于揭示这种差异的成因与影响。局部分子钟（local-clock，即基于系统发育树若干分支估算得到的分子进化速率）间的比较，是该研究领域的常用分析手段。本文指出，当前常用的似然比检验（Likelihood Ratio Test, LRT）在绝大多数情形下无法用于局部分子钟比较的统计有效性验证。对此，本文提出局部分子钟置换检验（local-clock permutation test, LCPT），这一简便方法可用于检验局部分子钟间差异的显著性。局部分子钟置换检验还可用于检验系统发育树各分支所对应任意参数间的差异显著性。基于模拟数据的验证结果表明，局部分子钟置换检验具备良好的局部分子钟差异检测效力。