© 2008 Society of Systematic Biologists
Trees of Trees: An Approach to Comparing Multiple Alternative Phylogenies
School of Mathematics and Statistics, Newcastle University Newcastle, UK; E-mail: tom.nye{at}ncl.ac.uk
Edited by Olivier Gascuel
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Abstract |
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Phylogenetic analysis very commonly produces several alternative trees for a given fixed set of taxa. For example, different sets of orthologous genes may be analyzed, or the analysis may sample from a distribution of probable trees. This article describes an approach to comparing and visualizing multiple alternative phylogenies via the idea of a "tree of trees" or "meta-tree." A meta-tree clusters phylogenies with similar topologies together in the same way that a phylogeny clusters species with similar DNA sequences. Leaf nodes on a meta-tree correspond to the original set of phylogenies given by some analysis, whereas interior nodes correspond to certain consensus topologies. The construction of meta-trees is motivated by analogy with construction of a most parsimonious tree for DNA data, but instead of using DNA letters, in a meta-tree the characters are partitions or splits of the set of taxa. An efficient algorithm for meta-tree construction is described that makes use of a known relationship between the majority consensus and parsimony in terms of gain and loss of splits. To illustrate these ideas meta-trees are constructed for two datasets: a set of gene trees for species of yeast and trees from a bootstrap analysis of a set of gene trees in ray-finned fish. A software tool for constructing meta-trees and comparing alternative phylogenies is available online, and the source code can be obtained from the author.
Keywords: Alternative phylogenies; consensus tree; median tree; parsimony; split; topology
Received October 3, 2007; Revised December 21, 2007; Accepted June 4, 2008
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