Date of this Version
The preferred interpretation of a phylogenetic tree is as a depiction of lines of descent. That is, trees communicate the evolutionary relationships among elements, such as genes or species, that connect a sample of branch tips. Under this interpretation, the nodes (branching points) on a tree are taken to correspond to actual biological entities that existed in the past: ancestral populations or ancestral genes. However, tree diagrams are also used in many nonevolutionary contexts, which can cause confusion. For example, trees can depict the clustering of genes on the basis of their expression profiles from microarrays, or the clustering of ecological communities by species composition. The prevalence of such cluster diagrams may explain why phylogenetic trees are often misinterpreted as depictions of the similarity among the branch tips. Phylogenetic trees show historical relationships, not similarities.