Polyhedral Geometry of Phylogenetic Rogue Taxa
Polyhedral Geometry of Phylogenetic Rogue Taxa
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DOI：
10.1007/s11538-010-9556-x
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发表时间：
2011-06-01
影响因子：
3.5
通讯作者：
Matsen, Frederick A.
中科院分区：
文献类型：
--
作者：
Cueto, Maria Angelica;Matsen, Frederick A.
遗传学家们都知道，在一个数据集中增加一个额外的分类单元（例如物种）可以以令人惊讶的方式改变最佳系统发育树的结构。然而，人们对这种“流氓分类群”效应知之甚少。在本文中，我们的行为特征的平衡最小进化（BME）遗传学的这种类型的数据集上使用工具，从多面体几何。首先，我们表明，对于任何距离矩阵存在的距离，一个“流氓分类”，这样的BME最优树的数据集与新的分类不包含任何非平凡的分裂（bipartitions）的原始数据的最优树。其次，我们证明了一个定理，限制这种类型的数据集的BME-最优树的拓扑结构，从而表明，一个流氓类群不能有任意的最优树的影响。第三，我们计算构建多面体圆锥体，当我们的原始数据适合四，五，六个分类群的树时，给出BME流氓分类群行为的完整答案。我们使用这些锥来推导出四个类群的流氓分类单元行为的充分条件，并通过模拟来了解流氓分类单元效应的频率。
It is well known among phylogeneticists that adding an extra taxon (e.g. species) to a data set can alter the structure of the optimal phylogenetic tree in surprising ways. However, little is known about this "rogue taxon" effect. In this paper we characterize the behavior of balanced minimum evolution (BME) phylogenetics on data sets of this type using tools from polyhedral geometry. First we show that for any distance matrix there exist distances to a "rogue taxon" such that the BME-optimal tree for the data set with the new taxon does not contain any nontrivial splits (bipartitions) of the optimal tree for the original data. Second, we prove a theorem which restricts the topology of BME-optimal trees for data sets of this type, thus showing that a rogue taxon cannot have an arbitrary effect on the optimal tree. Third, we computationally construct polyhedral cones that give complete answers for BME rogue taxon behavior when our original data fits a tree on four, five, and six taxa. We use these cones to derive sufficient conditions for rogue taxon behavior for four taxa, and to understand the frequency of the rogue taxon effect via simulation.