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-based names 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 the two kinds of names and trees and should therefore be amended to adopt one or the other of the two kinds of trees and the corresponding kind of names. In this contribution, I accept the distinction between the two kinds of phylogenetic trees described by Martin et al. (2010), as well as their equivalency with regard to contained phylogenetic information. Nevertheless, I argue that the names applied to the different kinds of trees by Martin et al. (2010) are inappropriate, and I propose more appropriate names for them. I then argue that Martin et al.'s (2010) conclusions concerning the applicability of node-and branch-based names in the context of what those authors called " node-" and " branch-based " trees are erroneous and result from assuming inappropriate taxon compositions (i.e., ones that would not be deduced from [standard] node-and branch-based phylogenetic definitions). Contrary to Martin et al. (2010), I argue that it is appropriate to apply both node-and branch-based phylogenetic definitions in the context of both " node-" and " branch-based " trees. Next, I show that the PhyloCode explicitly adopts trees similar to those that Martin et al. (2010) call " branch-based " and that the inappropriate circumscriptions adopted by those authors are related to their overlooking that fact. Nevertheless, I argue that the term " branch-based definition " is inappropriate in the context of " node-based " trees, and I propose alternative names for both kinds of definitions that are applicable in the context of both kinds of trees. Finally, I argue that what have previously been called " node-based " definitions are most appropriate for defining the names of crown clades while definitions previously termed " branch-based " …