In cladistic analysis, the inference of homology has been previously suggested to be at least a two-step procedure: the first step is the hypothesis of correspondence of constituent features between two or more organisms. The second step subject these character hypotheses to the test of congruence (Rieppel & Kearney, 2002). In this sense it is not just the method used for phylogenetic inference which determines the quality of relationship hypotheses. Definition and selection of characters constitute a fundamental step (in the relationship hypotheses), because with them the crucial test in phylogenetic analysis is done.
A character is a logical relation established between intrinsic attributes of two or more organisms that is rooted in observation (Rieppel, 1988). So, “a meaningful character is thus based upon a character description that can in itself be evaluated... and potentially rejected” (Riepperl & Kearney, 2002). In morphological data, there are some classical characteristics that a good character must have: topology, connectivity, and the establishment of a one-to-one relationship of the parts being compared (Rieppel & Kearney, 2002). Although, there are other attributes as function and “special similarity” that are relevant in character definition (Rieppel & Kearney, 2002; Agnarsson & Coddington, 2007). Sometimes, topology correspondence, function and special similarity could conflict and quantitative methods for choosing among different criteria are necessary (Agnarsson & Coddington, 2007).
Other problem that morphological data face is coding. When we compare features in different organisms in some way, we are assuming some correspondence (not necessary topological). So, a presence-absence coding (See Pleijel, 1999) is telling nothing about that feature correspondence, and nothing about the taxa relationship. Becasuse, what forms the evidence in a cladistic analysis is the change among the character states, not the existence of different states (Brower, 2000).
In molecular data, the problem of character definition and character coding is different. Because it is widely accepted that similarity is equivalent to homology, but as those data also have homoplasy, similarity could not be seen as homology. Therefore, a criterion for defining molecular character hypotheses is necessary (de Pinna, 1991). The characters definition with DNA (or other molecular data) could be seen as a previous step, aligning with an algorithm. Or could be seen as a direct search of the optimal trees via direct optimization of the data with which the character hypotheses change during the search (Wheeler, 1996). The second approach is preferable, while it is testing the topology directly and is exploring different possibilities of the data, not just an alignment.
Finally, congruence is the test that corroborates the character as synapomorphies. The tool that allow to asses hypotheses of relationship, and concomitantly of character evolution, is parsimony. Parsimony maximizes congruence between the characters, so it maximizes the propositions of homology (Farris, 1983; Kluge, 1997; Sober, 1998).
Agnarsson, I. & Coddington, J. A. 2007. Quantitative tests of primary homology. Cladistics.
Brower, A. 2000. Homology and the inference of systematic relationships: some historical and philosophical perspectives. In Homology and systematics, coding characters for phylogenetic analysis (eds. Scotland, R & Pennington, R. T.). Taylor & Francis.
de Pinna, M. C. C. 1991. Concepts and tests of homology in the cladistic paradigm. Cladistics.
Kluge, A. 1997. Testability and the refutation and corroboration of cladistic hypotheses. Cladistics.
Pleijel, F. 1995. On character coding for phylogenetic reconstruction. Cladistics.
Rieppel, O. & Kearney, M. 2002. Similarity. Biological Journal of the Linnean Society.
Wheeler, W. C. 1996. Optimization alignment: the end of multiple sequence alignment in phylogenetics? Cladistics.
Farris SJ. 1983. The logical basis of phylogenetic analysis. In: Platnick, NI, Funk, VA, eds. Advances in Cladistics, Vol. 2. New York: Columbia University Press.