BOOTSTRAP CONFIDENCE LEVELS FOR PHYLOGENETIC TREES

Evolutionary trees are often estimated from DNA or RNA sequence data, How much confidence should we have in the estimated trees? In 1985, Fe lsenstein [Felsenstein, J. (1985) Evolution 39, 783-791] suggested the use of the bootstrap to answer this question. Felsenstein's method, w hich in concept is a straightforward application of the bootstrap, is widely used, but has been criticized as biased in the genetics literat ure. This paper concerns the use of the bootstrap in the tree problem. We shown that Felsenstein's method is not biased, but that it can be corrected to better agree with standard ideas of confidence levels and hypothesis testing. These corrections can be made by using the more e laborate bootstrap method presented here, at the expense of considerab ly more computation.