BOOTSTRAP METHOD OF INTERIOR-BRANCH TEST FOR PHYLOGENETIC TREES

Statistical properties of the bootstrap test of interior branch length s of phylogenetic trees have been studied and compared with those of t he standard interior-branch test in computer simulations. Examination of the properties of the tests under the null hypothesis showed that b oth tests for an interior branch of a predetermined topology are quite reliable when the distribution of the branch length estimate approach es a normal distribution. Unlike the standard interior-branch test, th e bootstrap test appears to retain this property even when the substit ution rate varies among sites. In this case, the distribution of the b ranch length estimate deviates from a normal distribution, and the sta ndard interior-branch test gives conservative confidence probability v alues. A simple correction method was developed for both interior-bran ch tests to be applied for testing the reliability of tree topologies estimated from sequence data. This correction for the standard interio r-branch test appears to be as effective as that obtained in our previ ous study, though it is much simpler. The bootstrap and standard inter ior-branch tests for estimated topologies become conservative as the n umber of sequence groups in a star-like tree increases.