Nodes, Branches, and Phylogenetic Definitions

Adopting the perspective of graph theory,Martin et al. (2010) described two kinds of phylogenetic trees, which they termed node-based and stem- or branch-based, that differ with respect to the biological interpretations of their component nodes and branches. After establishing equivalency between the two different kinds of trees in terms of encoded information regarding taxa and their phylogenetic relationships, Martin et al. (2010) argued that node-basednames should be applied only in the context of node-based trees, and that branch-based names should be applied only in the context of branch-based trees, because node-based names cannot exist on branch-based trees and vice versa. They also suggested that the International Code of Phylogenetic Nomenclature or PhyloCode (Cantino and de Queiroz 2010) confuses th