FREUDENSTEIN, JOHN V.* and MARK P. SIMMONS. Herbarium and Dept. of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43212. - Artifacts of coding amino acids and other composite characters for phylogenetic analysis.
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