The Effects of Partitioning on Phylogenetic Inference
The Effects of Partitioning on Phylogenetic Inference
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DOI：
10.1093/molbev/msv026
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发表时间：
2015-06-01
影响因子：
10.7
通讯作者：
Lanfear, Robert
中科院分区：
文献类型：
--
作者：
Kainer, David;Lanfear, Robert
分区是系统发育中常用的一种方法，旨在适应位点之间替代模式的变化。尽管它很受欢迎，但很少有系统的研究它对系统发育推断的影响，也没有研究比较不同方法对许多经验数据集的划分的影响。在这项研究中，我们应用了四种常用的方法对34个经验数据集进行分区，然后比较了使用每种方法估计的树拓扑结构、分支长度和bootstrap支持度。我们发现分区方案的选择经常影响树的拓扑结构，特别是当分区被省略时。最值得注意的是，我们偶尔会发现使用次优分区方案会在树中产生高度支持但不正确的节点。分支长度和引导支持也受到分区方案选择的影响，有时影响很大。我们讨论了产生这些影响的原因，并为最佳实践提出了一些建议。
Partitioning is a commonly used method in phylogenetics that aims to accommodate variation in substitution patterns among sites. Despite its popularity, there have been few systematic studies of its effects on phylogenetic inference, and there have been no studies that compare the effects of different approaches to partitioning across many empirical data sets. In this study, we applied four commonly used approaches to partitioning to each of 34 empirical data sets, and then compared the resulting tree topologies, branch-lengths, and bootstrap support estimated using each approach. We find that the choice of partitioning scheme often affects tree topology, particularly when partitioning is omitted. Most notably, we find occasional instances where the use of a suboptimal partitioning scheme produces highly supported but incorrect nodes in the tree. Branch-lengths and bootstrap support are also affected by the choice of partitioning scheme, sometimes dramatically so. We discuss the reasons for these effects and make some suggestions for best practice.