Duchêne Sebastián, Ho Simon Y W
School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia.
School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia.
Mol Phylogenet Evol. 2014 Aug;77:65-70. doi: 10.1016/j.ympev.2014.04.010. Epub 2014 Apr 18.
Molecular data sets comprising DNA sequences from multiple genes are now commonplace in phylogenetic studies. These data sets should be analysed using methods that can account for heterogeneity in the molecular evolutionary process among genes. A common problem is determining how many evolutionary models should be applied to subsets of the data. Different genes can exhibit differing patterns of rate variation among lineages, making it appropriate to assign a separate molecular-clock model to each subset of the data (i.e., a 'partitioned' clock model). The impact of clock-partitioning on estimates of evolutionary rates and timescales is largely unknown. In this study, we use a recently developed method, ClockstaR, to evaluate the effect of using different clock-partitioning schemes. We conduct Bayesian phylogenetic analyses of simulated and empirical multigene data sets. Our analyses show strong statistical support for the clock-partitioning scheme chosen by ClockstaR. In addition, we find that the optimal clock-partitioning scheme produces more reliable estimates of node ages than other schemes.
在系统发育研究中，包含多个基因DNA序列的分子数据集如今已很常见。这些数据集应使用能够考虑基因间分子进化过程异质性的方法进行分析。一个常见问题是确定应将多少种进化模型应用于数据子集。不同基因在谱系间可能表现出不同的速率变化模式，因此为数据的每个子集分配一个单独的分子钟模型（即“分区”钟模型）是合适的。时钟分区对进化速率和时间尺度估计的影响在很大程度上尚不清楚。在本研究中，我们使用一种最近开发的方法ClockstaR来评估使用不同时钟分区方案的效果。我们对模拟和实证多基因数据集进行贝叶斯系统发育分析。我们的分析为ClockstaR选择的时钟分区方案提供了强有力的统计支持。此外，我们发现最优时钟分区方案比其他方案能产生更可靠的节点年龄估计。
