Calibrating the bootstrap test of monophyly.

It has been suggested that the bootstrap test of monophyly is too conservative, i.e. the test rejects the hypothesis of monophyly when it is true far too often. Here, a method called the iterated bootstrap is described which estimates by randomization the probabilities associated with rejecting the hypothesis of monophyly when it is true and accepting the hypothesis of monophyly when it is false. Using this method, the bootstrap test can be calibrated by taking account of the errors associated with the hypothesis test. This method is applied to the high-level phylogeny of the Platyhelminthes using 18S rRNA sequences. The analysis suggests that the data cannot unequivocally resolve the placement of the Platyhelminthes with respect to the Annelida and Insecta.

[1]  J. Felsenstein.  CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.

[2]  J. Bull,et al.  Experimental phylogenetics: generation of a known phylogeny. , 1992, Science.

[3]  J. Cheverud,et al.  THE QUANTITATIVE ASSESSMENT OF PHYLOGENETIC CONSTRAINTS IN COMPARATIVE ANALYSES: SEXUAL DIMORPHISM IN BODY WEIGHT AMONG PRIMATES , 1985, Evolution; international journal of organic evolution.

[4]  Mark Kot,et al.  Adaptation: Statistics and a Null Model for Estimating Phylogenetic Effects , 1990 .

[5]  B. Efron,et al.  A Leisurely Look at the Bootstrap, the Jackknife, and , 1983 .

[6]  R. Raff,et al.  Molecular phylogeny of the animal kingdom. , 1988, Science.

[7]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[8]  P. Hall,et al.  On bootstrap resampling and iteration , 1988 .

[9]  M. Pagel,et al.  The comparative method in evolutionary biology , 1991 .

[10]  D Penny,et al.  Estimating the reliability of evolutionary trees. , 1986, Molecular biology and evolution.

[11]  M. Nei,et al.  Estimation of evolutionary distance between nucleotide sequences. , 1984, Molecular biology and evolution.

[12]  Joseph Felsenstein,et al.  Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters , 1973 .

[13]  Michael J Sanderson,et al.  CONFIDENCE LIMITS ON PHYLOGENIES: THE BOOTSTRAP REVISITED , 1989, Cladistics : the international journal of the Willi Hennig Society.