Novel versus unsupported clades: Assessing the qualitative support for clades in MRP supertrees
Novel versus unsupported clades: Assessing the qualitative support for clades in MRP supertrees
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DOI：
10.1080/10635150390252242
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发表时间：
2003-12-01
影响因子：
6.5
通讯作者：
Bininda-Emonds, ORP
中科院分区：
文献类型：
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作者：
Bininda-Emonds, ORP
矩阵表示与简约（MRP）超树结构一直受到批评，因为超树可能指定的分支是矛盾的每一个源树有助于它。这种不支持的分支也可能出现使用其他超树方法;然而，他们的发病率在很大程度上是未知的。在这项研究中，我调查了模拟和经验MRP超树中不支持分支的频率。在这里，我提出了一个新的索引，QS，量化的超树和它的分支之间的源树集的定性支持。结果表明，不支持的分支是非常罕见的MRP超树，发生时，最经常有几个源树，都拥有相同的一套类群。然而，即使在这些条件下，未支持的分支的频率<0.2%。食肉目和兔形目超级树都没有不支持的分支，反映了两者都使用了大量的源树。建议的QS指数与另一种定量分支支持措施（自举频率，来自MRP矩阵的重新排序）广泛相关，但似乎更敏感。更重要的是，它们在源树的级别上采样，因此，与引导不同，它们适合于总结MRP超树分支的支持。
Matrix representation with parsimony ( MRP) supertree construction has been criticized because the supertree may specify clades that are contradicted by every source tree contributing to it. Such unsupported clades may also occur using other supertree methods; however, their incidence is largely unknown. In this study, I investigated the frequency of unsupported clades in both simulated and empirical MRP supertrees. Here, I propose a new index, QS, to quantify the qualitative support for a supertree and its clades among the set of source trees. Results show that unsupported clades are very rare inMRP supertrees, occurring most often when there are few source trees that all possess the same set of taxa. However, even under these conditions the frequency of unsupported clades was < 0.2%. Unsupported clades were absent from both the Carnivora and Lagomorpha supertrees, reflecting the use of large numbers of source trees for both. The proposed QS indices are correlated broadly with another measure of quantitative clade support ( bootstrap frequencies, as derived from resampling of the MRP matrix) but appear to be more sensitive. More importantly, they sample at the level of the source trees and thus, unlike the bootstrap, are suitable for summarizing the support of MRP supertree clades.