Does minimizing homoplasy really maximize homology? MaHo: A method for evaluating homology among most parsimonious trees

Parsimony analysis aims at finding the tree that best fits hypotheses of homology. However, parsimony does not directly maximize homology, but minimizes homoplasy. When a parsimony analysis results in more than a single most-parsimonious tree (MPT), it is shown that the number of homologous characters may vary significantly. We propose a method called MaHo to identify, among the MPTs, the tree(s) that has (have) the highest number of characters that are homologies. We apply this approach to the phylogenetic relationships of the Dombeyoideae (Malvaceae) of the Mascarene Islands. A parsimony analysis was performed, including 31 representatives of the Dombeyoideae. The search resulted in 29,336 MPTs. MaHo was used in order to improve the resolution of the consensus and to increase the number of unambiguous homologies. The consensus of the 7592 MPTs presenting the highest number of homologies was chosen. This resulted in unravelling five additional synapomorphies and in reducing the number of MPTs.