The Soltis et al. (2000) 567-terminal simultaneous analysis of atpB, rbcL, and 18S rDNA was used as an empirical example to test the use of amino acid vs. nucleotide characters for protein-coding genes at deeper taxonomic levels. Nucleotide characters for atpB and rbcL have 6.5 times the amount of possible synapomorphy as amino acid characters. The nucleotide-based jackknife tree is much more resolved than the amino acid-based tree, for both large and small clades. Nearly twice the percentage of well supported clades resolved in the 18S rDNA tree are resolved using nucleotide characters (88.5%) relative to amino acid characters (47.5%). The well supported clades resolved by both character types are much better supported by nucleotide characters (98.6% vs. 83.3% average jackknife support). Nucleotide characters outperform amino acid characters even when both matrices are reduced to the same amount of possible synapomorphy (236 randomly selected informative nucleotide characters vs. all 411 informative amino acid characters). For the reduced nucleotide-based matrix, 72.1% of the well supported clades are resolved, and the well supported clades resolved by both character types are better supported by nucleotide characters (92.7% vs. 85.9% average jackknife support). Although the performance of nucleotide characters decreased with reduced sampling of terminals, amino acid characters did not improve. Nucleotide characters outperformed amino acid characters even with 90% of the terminals deleted, in order to increase genetic distance between clades. Of the 14 cases of conflicting resolution between the amino acid and nucleotide-based jackknife trees, there is independent evidence for the phylogeny of 11 these groups. For 10 of the 11 cases, the independent evidence supports the nucleotide-based topology. There is evidence of convergence to the same amino acid specified by different codons and/or artifacts caused by the use of composite characters for the amino acid characters supporting eight of these contradictory clades.

Key words: amino acid, angiosperm phylogeny, atpB, character coding, phylogenetic information, rbcL