COMPARING PATTERNS OF NUCLEOTIDE SUBSTITUTION RATES AMONG CHLOROPLASTLOCI USING THE RELATIVE RATIO TEST

Even when several genetic loci are used in molecular evolutionary stud ies, each locus is typically analyzed independently of the others. Thi s type of approach makes it difficult to study mechanisms and processe s that affect multiple genes. In this work we develop a statistical ap proach for the joint analysis of two or more loci. The tests we propos e examine whether or not nucleotide substitution rates across evolutio nary lineages have the same relative proportions at two loci. Theses p rocedures are applied to 33 genes from the chloroplast genomes of rice , tobacco, pine, and liverwort. With the exception of five clearly dis tinct loci, we find that synonymous substitution rates tend to change proportionally across genes. We interpret these results to be consiste nt with a ''lineage effect'' acting on the entire chloroplast genome. In contrast, nonsynonymous rates do not change proportionally across g enes, suggesting that locus-specific evolutionary effects dominate pat terns of nonsynonymous substitution.