Analysis and Visualization of Tree Space

We explored the use of multidimensional scaling (MDS) of tree-to-tree pairwise distances to visualize the relationships among sets of phylogenetic trees. We found the technique to be useful for exploring “tree islands” (sets of topologically related trees among larger sets of near-optimal trees), fo...

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Bibliographic Details
Published in:Systematic biology 2005-06, Vol.54 (3), p.471-482
Main Authors: Hillis, David M., Heath, Tracy A., John, Katherine St, Anderson, Frank
Format: Article
Language:English
Subjects:
Bayes Theorem
Bayesian analysis
Bioinformatics
Bootstrap resampling
Classification - methods
Data Interpretation, Statistical
Data visualization
Datasets
Evolutionary biology
Genetic diversity
Markov chains
Modeling
Multidimensional scaling
phylogenetic analysis
Phylogenetics
Phylogeny
Scientific method
Simulations
Software
tree space
visualization
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Summary:We explored the use of multidimensional scaling (MDS) of tree-to-tree pairwise distances to visualize the relationships among sets of phylogenetic trees. We found the technique to be useful for exploring “tree islands” (sets of topologically related trees among larger sets of near-optimal trees), for comparing sets of trees obtained from bootstrapping and Bayesian sampling, for comparing trees obtained from the analysis of several different genes, and for comparing multiple Bayesian analyses. The technique was also useful as a teaching aid for illustrating the progress of a Bayesian analysis and as an exploratory tool for examining large sets of phylogenetic trees. We also identified some limitations to the method, including distortions of the multidimensional tree space into two dimensions through the MDS technique, and the definition of the MDS-defined space based on a limited sample of trees. Nonetheless, the technique is a useful approach for the analysis of large sets of phylogenetic trees.
ISSN:1063-5157
1076-836X
DOI:10.1080/10635150590946961