Jin Yuanting, Brown Richard P
College of Life Sciences, China Jiliang University, Hangzhou, 310018, PR China.
School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, L3 3AF, UK.
Cladistics. 2018 Oct;34(5):568-573. doi: 10.1111/cla.12223. Epub 2017 Nov 12.
More loci/partitions should improve Bayesian estimation of divergence times on phylogenies but it has recently been shown that this can lead to surprisingly poor estimation due to the way it affects the prior on mean substitution rate. Here we consider the likely impact of partition number on divergence time analyses carried out using the program BEAST. Mitochondrial genome data from toad-headed lizards (genus Phrynocephalus) from the Qinghai-Tibetan Plateau were used to examine this effect. Under increased partitioning of the sequences, BEAST posterior divergence times became unreasonably narrow and downwardly biased due to misspecification of the mean substitution rate prior. This effect was detectable when relatively few partitions were used (i.e. between four and eight), but became very acute for 27-86 partitions. Fortunately, a correction that adjusts the standard deviation of the mean of locus rates led to results that were equivalent to those obtained using the latest version of the program MCMCtree, which implements a new gamma-Dirichlet prior to overcome this problem. A review of the literature shows that a substantial number of BEAST dating studies are likely to have been affected by this misspecification of the rate prior.
更多的基因座/分区应该会改善系统发育树上分歧时间的贝叶斯估计，但最近的研究表明，由于其对平均替换率先验的影响方式，这可能会导致惊人的糟糕估计。在这里，我们考虑分区数量对使用BEAST程序进行的分歧时间分析的可能影响。来自青藏高原沙蜥属（Phrynocephalus）的线粒体基因组数据被用于检验这种影响。在序列分区增加的情况下，由于平均替换率先验的错误设定，BEAST的后验分歧时间变得不合理地狭窄且向下偏移。当使用相对较少的分区（即4到8个之间）时，这种影响就可以检测到，但对于27 - 86个分区来说变得非常严重。幸运的是，一种调整基因座速率均值标准差的校正方法得出的结果与使用实现了新的伽马 - 狄利克雷先验以克服此问题的最新版本程序MCMCtree所获得的结果相当。对文献的综述表明，大量的BEAST定年研究可能受到了这种速率先验错误设定的影响。
