A phylogenetic analysis can be no better than the homology hypotheses on which it is based. Care must be taken both in formulating these hypotheses and in their formalization - i.e., character coding. 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 independent characters that occurs during the construction of composite-character states creates putative synapomorphies that were not present in the independent characters. For codon and 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 using reductive coding may be resolved as monophyletic using composite coding. In addition to the problem with artificial resolution caused by the use of composite characters, amino-acid characters are subject to loss of information and convergence caused by different codons specifying the same amino acid. The artificial character states indicated by the amino-acid characters are unlikely to be congruent with the true gene tree, and therefore, these artificial character states are likely to be homoplasious. Amino-acid characters have been considered to be more conservative than nucleotide characters. While the intent may be one of conservatism, the actual effect, with the complications caused by the use of composite characters, is not.

Key words: amino acid, character coding, nucleotide, phylogenetic analysis