Artifacts of Coding Amino Acids and Other Composite Characters for Phylogenetic Analysis

A phylogenetic analysis can be no better than the characters on which it is based. Just as it is inappropriate to code character states of individual characters as separate presence/absence characters, it is inappropriate to combine independent characters because not all information in the data is being utilized. Composite characters link otherwise discernible states from different characters together to form new character states. There are two related problems with this coding. First, there is a loss of hierarchic information between the reductive and composite characters when unordered states are used. Second, the linking of separate characters that occurs during the construction of composite character states can create putative synapomorphies that were not present in the separate characters. For amino acid characters, the problem may occur whenever more than one position of a codon is variable among the terminals sampled. Groups that are resolved as paraphyletic with reductive coding may be resolved as monophyletic with composite coding. The artificial character states indicated by the amino acid characters are unlikely to be congruent with the true gene tree.