Simulating and detecting autocorrelation of molecular evolutionary rates among lineages
Simulating and detecting autocorrelation of molecular evolutionary rates among lineages
复制标题
DOI：
10.1111/1755-0998.12320
复制
发表时间：
2015-07-01
影响因子：
7.7
通讯作者：
Duchene, David
中科院分区：
文献类型：
--
作者：
Ho, Simon Y. W.;Duchene, Sebastian;Duchene, David
进化时间尺度可以使用基于分子钟的系统发育方法从遗传数据中估计。为了解释谱系之间的分子速率变化，已经开发了一些弛豫时钟模型。这些模型中的一些假设比率在谱系之间以自相关的方式变化，因此密切相关的物种具有相似的比率。相反，不相关的松弛时钟允许从单个分布中提取所有分支特定的速率，而不假设沿沿着分支的速率之间存在任何相关性。这两类弛豫时钟模型中哪一类更适合生物数据还不确定。我们提出了一个R软件包，NELSI，它允许DNA序列的进化模拟根据一系列的时钟模型。使用该软件包生成的数据，我们评估了两种贝叶斯系统发育方法区分不同的松弛时钟模型和量化谱系之间的速率变化的能力。我们的分析结果表明，率自相关通常是很难检测，即使有完整的分类单元采样。这为过去未能在一系列数据集中检测到速率自相关提供了一个潜在的解释。
Evolutionary timescales can be estimated from genetic data using phylogenetic methods based on the molecular clock. To account for molecular rate variation among lineages, a number of relaxed-clock models have been developed. Some of these models assume that rates vary among lineages in an autocorrelated manner, so that closely related species share similar rates. In contrast, uncorrelated relaxed clocks allow all of the branch-specific rates to be drawn from a single distribution, without assuming any correlation between rates along neighbouring branches. There is uncertainty about which of these two classes of relaxed-clock models are more appropriate for biological data. We present an R package, NELSI, that allows the evolution of DNA sequences to be simulated according to a range of clock models. Using data generated by this package, we assessed the ability of two Bayesian phylogenetic methods to distinguish among different relaxed-clock models and to quantify rate variation among lineages. The results of our analyses show that rate autocorrelation is typically difficult to detect, even when there is complete taxon sampling. This provides a potential explanation for past failures to detect rate autocorrelation in a range of data sets.