Is there a justification for differential a priori weighting in coding sequences? A case study from rbcL and...

Functional constraints are often assumed to influence the performance of nucleotide characters in phylogenetic analysis: First and second codon positions and sites of structural importance are considered to show less homoplasy. We investigate the performance of rbcL characters with differential functional constraints in a cladistic analysis of the plant family Apocynaceae s.l. (Sennblad and Bremer, in prep.). Performance is measured as rescaled consistency indices (rc). We show there is no significant difference in performance between parsimony-informative sites constrained by function in the enzyme, and sites that are not. Furthermore, the substitutions in third-codon position performed significantly better than those in first and second. The variation of rc within the different classes was high, however. Consequently, there is no support for routinely applied a priori differential weighting, neither of codon positions, nor of different functional classes from the present analysis of rbcL data in the Apocynaceae s.l.