© 2005 Society of Systematic Biologists
Visualizing Conflicting Evolutionary Hypotheses in Large Collections of Trees: Using Consensus Networks to Study the Origins of Placentals and Hexapods
1 The Allan Wilson Centre for Molecular Ecology and Evolution, Massey University Private Bag 11 222, Palmerston North, New Zealand E-mail: b.r.holland{at}massey.ac.nz
2 The Linnaeus Centre for Bioinformatics, Uppsala University Sweden
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Abstract |
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Many phylogenetic methods produce large collections of trees as opposed to a single tree, which allows the exploration of support for various evolutionary hypotheses. However, to be useful, the information contained in large collections of trees should be summarized; frequently this is achieved by constructing a consensus tree. Consensus trees display only those signals that are present in a large proportion of the trees. However, by their very nature consensus trees require that any conflicts between the trees are necessarily disregarded. We present a method that extends the notion of consensus trees to allow the visualization of conflicting hypotheses in a consensus network. We demonstrate the utility of this method in highlighting differences amongst maximum likelihood bootstrap values and Bayesian posterior probabilities in the placental mammal phylogeny, and also in comparing the phylogenetic signal contained in amino acid versus nucleotide characters for hexapod monophyly.
Keywords: Bayesian posterior probabilities; consensus trees; hexapods; median networks; nonparametric bootstrap; placental mammals; phylogenetic trees; quartet puzzling
Received December 17, 2003; Revised August 3, 2004; Accepted September 12, 2004
3 Present Address: Département de Biochimie, Faculté de Médecine, Université de Montréal, Québec, Canada
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