FUNCTIONAL CONSTRAINTS AND RBCL EVIDENCE FOR LAND PLANT PHYLOGENY

Although the proportion of ''functional'' DNA in eukaryotic genomes is both debatable and subject to definition, most sequences gathered for phylogenetic purposes are indisputably functional. For example, patte rns of variation are likely to be strongly constrained in ribosomal RN As because of their structural and catalytic roles in protein translat ion, and in protein-coding genes, because of protein function itself. Although seemingly obvious, these concerns are usually ignored by work ers producing gene trees. We have examined the extent of functional co nstraints in land-plant rbcL sequences. Not only do rbcL sequences app ear to change with essentially clocklike regularity, but nucleotide-ba sed cladograms imply that approximately 97.5% of codon changes on inte rnal branches are functionally neutral (i.e., synonymous or functional ly labile). From this perspective, rbcL evolution appears to be strong ly constrained by function. Transforming nucleotide data into ad hoc s tring recognitions alters the size of the unit character sufficiently to highlight ''blocks'' of conservative information that may or may no t be functionally constrained. Simultaneous cladistic analysis of all available evidence will highlight the proportion of congruent informat ion, despite diverse functional constraints among the characters analy zed. We demonstrate the strength of this approach using different form s of the same rbcL evidence (i.e., nucleotides, strings, or amino acid s) in combination with the seed-plant data of Nixon et al.