ON TRANSITION BIAS IN MITOCHONDRIAL GENES OF POCKET GOPHERS

The relative contribution of mutation and purifying selection to trans ition bias has not been quantitatively assessed in mitochondrial prote in genes. The observed transition/transversion (s/v) ratio is (mu(s), P-s)/(mu(v) P-v), where mu(s) and mu(v) denote mutation rate of transi tions and transversions, respectively, and P-s and P-v denote fixation probabilities of transitions and transversions, respectively. Because selection against synonymous transitions can be assumed to be roughly equal to that against synonymous transversions, P-s/P-v approximate t o 1 at fourfold degenerate sites, so that the s/v ratio at fourfold de generate sites is approximately mu(s)/mu(v), which is a measure of mut ational contribution to transition bias. Similarly, the s/mu ratio at nondegenerate sites is also an estimate of mu(s)/mu(v) if we assume th at selection against nonsynonymous transitions is roughly equal to tha t against nonsynonymous transversions. In two mitochondrial genes, cyt ochrome oxidase subunit I (COI) and cytochrome b (cyt-b) in pocket gop hers, the s/v ratio is about two at nondegenerate and fourfold degener ate sites for both the COI and the cyt-b genes. This implies that muta tion contribution to transition bias is relatively small. In contrast, the s/v ratio is much greater at twofold degenerate sites, being 48 f or COI and 30 for cyt-b. Given that the mu(x)/mu(v) ratio is about 2, the P-s/P-v ratio at twofold degenerate sites must be on the order of 20 or greater. This suggests a great effect of purifying selection on transition bias in mitochondrial protein genes because transitions are synonymous and transversions are nonsynonymous at twofold degenerate sites in mammalian mitochondrial genes. We also found that nonsynonymo us mutations at twofold degenerate sites are more neutral than nonsyno nymous mutations at nondegenerate sites, and that the COI gene is subj ect to stronger purifying selection than is the cyt-b gene. A model is presented to integrate the effect of purifying selection, condon bias , DNA repair and GC content on s/v ratio of protein-coding genes.