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, Felsenstein [Felsenstein, J. (1985) Evolution 39, 783-791] suggested the use of the bootstrap to answer this question. Felsenstein's method, which in concept...

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Veröffentlicht in:Proceedings of the National Academy of Sciences - PNAS 1996-07, Vol.93 (14), p.7085-7090
Hauptverfasser: Efron, Bradley, Halloran, Elizabeth, Holmes, Susan
Format: Artikel
Sprache:eng
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Zusammenfassung:Evolutionary trees are often estimated from DNA or RNA sequence data. How much confidence should we have in the estimated trees? In 1985, Felsenstein [Felsenstein, J. (1985) Evolution 39, 783-791] suggested the use of the bootstrap to answer this question. Felsenstein's method, which in concept is a straightforward application of the bootstrap, is widely used, but has been criticized as biased in the genetics literature. This paper concerns the use of the bootstrap in the tree problem. We show 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 elaborate bootstrap method presented here, at the expense of considerably more computation.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.93.14.7085