An empirical test of the midpoint rooting method
An empirical test of the midpoint rooting method
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DOI：
10.1111/j.1095-8312.2007.00864.x
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发表时间：
2007-12-01
影响因子：
1.9
通讯作者：
De Moraes Russo, Claudia A.
中科院分区：
文献类型：
--
作者：
Hess, Pablo N.;De Moraes Russo, Claudia A.
外群方法广泛用于建立系统发育树。然而，准确的根指示在很大程度上取决于适当的外群的可用性。另一种生根方法是中点生根（MPR）。在这种情况下，根设置在两个最不同的操作分类单元之间的中点。尽管中点求根算法已被广泛使用，但该方法检索正确根的效率尚未经过测试。在本研究中，我们凭经验测试了 MPR 在获得给定系统发育树的外群根方面的成功率。这是通过消除来自 33 篇论文的 50 个选定数据集中的外群体并使用中点法对树进行生根来实现的。因此，我们能够比较每种方法检索到的根位置。数据集被分为具有不同根一致性的三类：具有单个外类群的数据集（MPR成功率为54％），具有多个外类群的数据集，其根位置不一致（82％的成功率），以及具有多个外类群的数据集，其中根位置一致（94％的成功率）。有趣的是，外群体根越一致，MPR 似乎就越成功。这有力地表明 MPR 方法是有价值的，特别是对于无法获得适当的外群的情况。 (c) 2007 年伦敦林奈学会。
The outgroup method is widely used to root phylogenetic trees. An accurate root indication, however, strongly depends on the availability of a proper outgroup. An alternate rooting method is the midpoint rooting (MPR). In this case, the root is set at the midpoint between the two most divergent operational taxonomic units. Although the midpoint rooting algorithm has been extensively used, the efficiency of this method in retrieving the correct root remains untested. In the present study, we empirically tested the success rate of the MPR in obtaining the outgroup root for a given phylogenetic tree. This was carried out by eliminating outgroups in 50 selected data sets from 33 papers and rooting the trees with the midpoint method. We were thus able to compare the root position retrieved by each method. Data sets were separated into three categories with different root consistencies: data sets with a single outgroup taxon (54% success rate for MPR), data sets with multiple outgroup taxa that showed inconsistency in root position (82% success rate), and data sets with multiple outgroup taxa in which root position was consistent (94% success rate). Interestingly, the more consistent the outgroup root is, the more successful MPR appears to be. This is a strong indication that the MPR method is valuable, particularly for cases where a proper outgroup is unavailable. (c) 2007 The Linnean Society of London.