Within-Terminal Steps and Fit Calculation—A Warning to Pee-Wee Users

Because Pee-Wee (version 2.5.1 and earlier versions) treats all within-terminal steps (internal steps) as homoplasies, if the command "ccode = (space).;" is in effect, it reports incorrect, and consistently too low, fit values for characters having states that occur only within polymorphic terminals (WPTO states). For matrices with WPTO states, this property of Pee-Wee may bias tree search in favour of characters having fewer WPTO states, other things being equal. Contrary to the intended purpose of the Goloboff criterion, Pee-Wee may even, in certain cases involving WPTO states, assign higher weight (fit) to characters with more homoplasy and therefore resolve character conflict in favour of less reliable characters.