Problems With Zero‐length Branches

In this note we call attention to a possibly common situation in which frequently used phylogenetic analysis and diagnosis programs may report cladograms that do not have support at every node from the data matrix analyzed to produce them. The problem involves branches that may or may not be interpreted as having zero length, the ambiguity arising from equally applicable but mutually exclusive alternative optimizations. Platnick et al. (1991) and Wilkinson (1995) commented on manifestations of the problem that involved missing entries and arbitrary resolutions, respectively. Wilkinson (1995) emphasized that programs can report topologies including zero-length branches even when no missing entries are present. However, Wilkinson posed the problem abstractly, a single character on one tree, addressed only one horn of the dilemma (branches ambiguously of zero or greater length were always assigned zero length), considered solutions only within the philosophical frame-work offered by PAUP, and offered no advice regarding what practicing system-atists could do to detect the problem. In addition, the treatment of the zero-length