The 'evolutionary signal' of homoplasy in protein-coding gene sequences and its consequences for a priori weighting in phylogeny.

To analyse independently homoplasy for the six possible types of substitution (i.e., A-G, C-T, A-C, A-T, C-G and G-T) at each of the three codon-positions of the cytochrome b gene, two approaches were used: the first is based on the consistency index which measures the amount of homoplasy, and the second is based on the saturation analysis which describes graphically the distribution of homoplasy within the taxonomic sampling. The results obtained from a data set of 32 sequences of Artiodactyla indicate that evolution of the cytochrome b is governed by differential constraints: 1) between the six substitutions-types, 2) between the three codon-positions, and 3) between the two mtDNA strands. Moreover, we find that non-synonymous sites can be more homoplastic than synonymous sites when the possibilities of substitutions are severely restricted because of the functional requirements of hydrophobicity. Most weighting schemes applied to protein-coding genes are elaborated from unjustified assumptions. We propose to weight each substitution-type at each codon-position according to its homoplasy content evaluated either with the consistency index or with an index representing the level of mutational saturation.