THE TRIPLES DISTANCE FOR ROOTED BIFURCATING PHYLOGENETIC TREES

We investigated the triples distance as a measure of the distance betw een two rooted bifurcating phylogenetic trees. The triples distance co unts the number of subtrees of three taxa that are different in the tw o trees. Exact expressions are given for the mean and variance of the sampling distribution of this distance measure. Also, a normal approxi mation is proved under the class of label-invariant models on the dist ribution of trees. The theory is applied to the usage of the triples d istance as a statistic for testing the null hypothesis that the simila rities in two trees can be explained by independent random structures. In an example, two phylogenies that describe the same seven species o f chloroccalean zoosporic green algae are compared: one phylogeny base d on morphological characteristics and one based on ribosomal RNA gene sequence data.