ABSTRACT
Phylogenetic trees are graphical representations of reconstructions of evolutionary histories. Each of the branches joins taxa (e.g., species) or sequences in a pattern that describes the distances between each of the taxa or sequences. Each of the taxa or sequences are dened as operational taxonomic units (OTUs; Figure 12.1) and appear on the terminal nodes of the tree. The branches joining them to other parts of the tree are called terminal branches, and all of the other branches are internal branches. Nodes are the points where branches meet. The root is the most ancient node. There are two general types of trees that can be drawn (Figure 12.2). The rst is a cladogram. In this tree, the branches are not always proportional to the distances between the OTUs. The branching is meant only to indicate the branching order among the OTUs. The second type of tree is a phylogram. These trees convey both the branching pattern and the distances among the OTUs. Trees can be produced that are slanted or rectangular in form. For rectangular phylograms, the horizontal branches convey the distances, while the vertical branches are only used to join
adjacent branches together. They contain no distance information. Circular trees are simply rectangular trees bent into a circle. All types of trees can be either rooted, when the location of the most ancient branch is known, or unrooted. However, changes in rooting can change the relationships as well as some of the distances, and, therefore, trees should be rooted only when their location is certain (Figure 12.3). Often this is done by including sister group into the analysis. A sister group is dened as an OTU that is closely related, but clearly outside of the group being analyzed. In this case, the sister group would be termed the outgroup and the group being analyzed would be the ingroup. Trees can be rotated at any of the nodes because this does not alter the relationships or the distances (Figure 12.4).
