CONFIDENCE-LIMITS ON PHYLOGENIES WITH A MOLECULAR CLOCK

For 3 spp. in the presence of a molecular clock, it is possible to compute how many steps a phylogeny must have to be significantly worse than the most parsimonious phylogeny. This analysis extends to the pioneering work by Cavender (1978, 1981) by taking advantage of the constraints imposed by the assumption of a molecular clock. The distribution of 2 statistics is obtained by direct enumeration of all possible outcomes in a worst-case phylogeny which has a trifurcation. The 2 statistics are the number of fewer steps in the best tree than in the next best tree, and the number of phylogenetically informative characters supporting the best trees. These 2 statistics are approximately equivalent in statistical power; tables of 95%-significance values are provided for each. The possible extension of these results to > 3 spp. is discussed. The enumeration of all outcomes also allows the computation of the exact tail probabilities for Templeton''s (1983) test of one tree against another. His test is not exactly correct, but usually is conservative when used as a 2-tailed test.