Figure 3. Comparison of the calculation of morphologic debt for polymorphic taxa in StrataPhy and MacClade. Character states for a single reconstructed character are represented by colors: yellow (state 0), blue (state 1), green (states 0&1), red (state 2), purple (states 1&2), brown (states 0&1&2), orange (states 2&3). Tick marks represent points at which units of debt are incurred, and accompanying boxes represent state transitions. For example, "+1" (Figure 3.1) indicates the derivation of state 1 in a newly polymorphic lineage, and "0->1" (Figure 3.3) indicates a transition from state 0 to state 1. The debt is shown for each three-taxon scenario. 3.1) In StrataPhy the ancestor of two polymorphic taxa with identical states is reconstructed to be polymorphic for those states as well. The only debt incurred in this example is on the lineage leading to this polymorphic ancestor, because its ancestor was not polymorphic. 3.2) MacClade assumes that the ancestor of two polymorphic taxa was monomorphic, and therefore requires two changes – the derivation of state 1 in each descendant. 3.3 and 3.4) In both StrataPhy and MacClade, if only one sister-taxon is polymorphic, then the ancestor is assumed to have only one state. In this case calculation of debt in StrataPhy is the same as in MacClade. 3.5) In StrataPhy, if two sister-taxa are both polymorphic, and share some, but not all of their states, the ancestor is reconstructed as being polymorphic for only the shared states. 3.6) As above, MacClade assumes that the ancestor of two polymorphic taxa has only one state, and therefore adds units of debt for each polymorphic state in each descendant. 3.7) In StrataPhy, if two polymorphic sister-taxa share only one state, then the ancestor is reconstructed as having only that state, and is not polymorphic. Units of debt are added for each unshared polymorphic state. 3.8) In StrataPhy, if two polymorphic sister-taxa do not share any states, then the ancestor is assumed to have only one of the observed states, although exactly which cannot be determined from only these two taxa. Units of debt are added for each observed state, minus one, for the undetermined ancestral state.