In classical taxonomic and phylogenetic literature, a monophyletic group, also called a clade, is defined as an assemblage that contains an ancestor and all its descendants. This term is most often applied to define groups of organisms that derive from a common ancestor, which form monophyletic taxa or clades (e.g., animals or cyanobacteria). However, it is used by molecular phylogeneticists also to define particular groups of DNA, RNA, or protein sequences in phylogenetic trees(e.g., different protein families derived from gene duplications). Monophyletic groups are based on the identification of synapomorphies, which are shared derived characters (e.g., a skull and a distinct head are synapomorphies of vertebrates). This criterion allows differentiating monophyletic groups from paraphyletic groups (those containing an ancestor and part of its descendants, such as the reptiles) and polyphyletic groups (those that do not contain the last common...