Weiss Gunter, von Haeseler Arndt
Max-Planck-Institut für evolutionäre Anthropologie, Leipzig, Germany.
Mol Biol Evol. 2003 Apr;20(4):572-8. doi: 10.1093/molbev/msg073. Epub 2003 Apr 2.
Phylogenetic tree reconstruction frequently assumes the homogeneity of the substitution process over the whole tree. To test this assumption statistically, we propose a test based on the sample covariance matrix of the set of substitution rate matrices estimated from pairwise sequence comparison. The sample covariance matrix is condensed into a one-dimensional test statistic Delta = sum ln(1 + delta(i)), where delta(i) are the eigenvalues of the sample covariance matrix. The test does not assume a specific mutational model. It analyses the variation in the estimated rate matrices. The distribution of this test statistic is determined by simulations based on the phylogeny estimated from the data. We study the power of the test under various scenarios and apply the test to X chromosome and mtDNA primate sequence data. Finally, we demonstrate how to include rate variation in the test.
系统发育树重建通常假定在整个树上替换过程是同质的。为了从统计学上检验这一假设，我们提出了一种基于从成对序列比较估计的替换率矩阵集的样本协方差矩阵的检验方法。样本协方差矩阵被压缩成一个一维检验统计量Δ = ∑ln(1 + δ(i))，其中δ(i)是样本协方差矩阵的特征值。该检验不假定特定的突变模型。它分析估计的速率矩阵中的变异。这个检验统计量的分布是通过基于从数据估计的系统发育的模拟来确定的。我们研究了在各种情况下该检验的功效，并将该检验应用于X染色体和线粒体DNA灵长类序列数据。最后，我们演示了如何在检验中纳入速率变异。
