 While character analysis and phylogenetic analysis are logically separate tasks, in theory they should be intertwined. A given phylogeny can make an assessment of homology more or less plausible. One proposal to avoid this problem is the introduction of a distinction between “primary” homologies (an initial character identification based on structural features) and “secondary” homologies (similarity due to common ancestry) which are inferred through phylogenetic analysis (Pinna 1991; see Roffe 2020 for a recent philosophical treatment of this distinction). On the other hand, Rieppel and Kearney (2002) argue that character hypotheses need to be independently testable and phylogenetic analysis can clearly provide evidence for miscoding of characters—even if this is not the intended goal.