The sequence of the region of the mitochondrial genome that encodes cytochrome oxidase subunit II (COII) has been determined for each of two closely related rat species, Rattus norvegicus and R. rattus. Comparison of the two sequences shows that 94.4% of the nucleotide substitutions are silent. The occurrence of this high proportion of silent substitutions leads us to propose that the rapid evolution of mtDNA relative to nuclear DNA is due only to silent changes and that amino acid-altering substitutions accumulate in nuclear and mtDNA at comparable rates. Other novel features of the nucleotide substitution pattern in the rat COII gene are a high transition/transversion ratio (8.0:1) and a strong bias toward C in equilibrium T transitions in the light strand. Comparison of the R. norvegicus COII sequence with the bovine and human sequences show that there may be selective constraints on some silent positions within the gene and that its rate of evolution may be different in different mammalian lineages.
