A note on Brazeau et al.'s (2017) algorithm for characters with inapplicable data, illustrated with an analysis of their Fig. 3d using anagallis, a program for parsimony analysis of character hierarchies

摘要

Brazeau et al. (2017) recently published a paper with a single-character algorithm to calculate the score of a character with inapplicable data on a tree, aiming to maximize homology in such characters. In this note, I show by example (using their Fig. 3d) that their algorithm is insufficient to find all optimal inner node state reconstructions in such characters. The root cause seems to be a inherent built-in constraint on the evaluation of implied absence/presence characters in their algorithm. In more complex cases, this constraint can lead to an overestimation of the optimal minimal score of character hierarchies and to errors in the trees that are selected as optimal during tree search.