Analysis and visualization of tree space

Abstract.—We explored the use of multidimensional scaling (MDS) of tree-to-tree pairwise distances to visualize the re-lationships 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 mul-tiple 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 defini-tion 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. [Bayesian analysis; multidimensional scaling; phylogenetic analysis; tree space; visualization.] Systematists are often faced with the need to analyze a large collection of phylogenetic trees. These trees may represent a collection of equally parsimonious solutions to a phylogenetic problem, or a set of trees of similar likelihood, or a sampled set of trees from a Marko