Ramírez, MJ (2007) Homology as a parsimony problem: a dynamic homology approach for morphological data. Cladistics 23 (6), 588–612.
"The primary data used to reconstruct phylogenies comes organized in the conceptual grid of homology correspondences, and the construction of this theory-rich grid depends in part on knowledge of relationships. This situation is not satisfactory as a conceptual system, because the evidence is not clearly delimited from the results. I explore the testing of alternative hypotheses of morphological correspondences in a quantitative cladistic context. The varying homology assessments implied by classical criteria of homology (topological equivalence, or position and connections; composition of structures, or commonality in details of construction) can be expressed as regular characters in a cladistic analysis. Doing so provides adequate transformation costs for changes in schemas of correspondences. Correspondences imply evolutionary transformations, and multiple schemas of correspondences can be compared according to the evolutionary transformations that they imply. The method is used to test the correspondences in sclerites of the male copulatory organs of spiders of the subfamily Amaurobioidinae (Arachnida, Araneae, Anyphaenidae). The correspondences of three sclerites are tested, in a data set of 93 species having one, two or three sclerites, using a simultaneous analysis of all the morphological characters. Most parsimonious trees are identified together with the correspondences they imply. Once the correspondences are integrated in the phylogenetic analysis, it is easy to evaluate the robustness of trees or decay in optimality after changes in anatomical interpretations. A Bremer support for anatomical interpretations is proposed, calculated as the increase in tree length when the specific interpretation is not used."