CODON BIAS IN ACTIN MULTIGENE FAMILIES AND EFFECTS ON THE RECONSTRUCTION OF PHYLOGENETIC-RELATIONSHIPS

Codon usage patterns and phylogenetic relationships in the actin multi gene family have been analyzed for three dipteran species-Drosophila m elanogaster, Bactrocera dorsalis, and Ceratitis capitata. In certain p hylogenetic tree reconstructions, using synonymous distances, some gen e relationships are altered due to a homogenization phenomenon. We pre sent evidence to show that this homogenization phenomenon is due to co don usage bias. A survey of the pattern of synonymous codon preference s for 11 actin genes from these three species reveals that five out of the six Drosophila actin genes show high degrees of codon bias as ind icated by scaled chi(2) values. In contrast to this, four out of the f ive actin genes from the other species have low codon bias values. A M onte Carlo contingency test indicates that for those Drosophila actin genes which exhibit codon bias, the patterns of codon usage are differ ent compared to actin genes from the other species. In addition, the g enes exhibiting codon bias also appear to have reduced rates of synony mous substitution. The homogenization phenomenon seen in terms of syno nymous substitutions is not observed for nonsynonymous changes. Becaus e of this homogenization phenomenon, ''trees'' constructed based on sy nonymous substitutions will be affected. These effects can be overt in the case of multigene families, but similar distortions may underlie reconstructions based on single-copy genes which exhibit codon usage b ias.