Estimation of the transition/transversion rate bias and species sampling

The transition/transversion (ti/tv) rate ratios are estimated by pairwise s equence comparison and joint likelihood analysis using mitochondrial cytoch rome b genes of 28 primate species, representing both the Strepsirrhini (le murs and lories) and the Anthropoidea (monkeys, apes, and humans). Pairwise comparison reveals a strong negative correlation between estimates of the ti/tv ratio and the sequence distance, even when both are corrected for mul tiple substitutions. The maximum-likelihood estimate of the ti/tv ratio cha nges with the species included in the analysis. The ti/tv bias within the l emuriform taxa is found to be as strong as in the anthropoids, in contradic tion to an earlier study which sampled only one lemuriform. Simulations sho w the surprising result that both the pairwise correction method and the jo int likelihood analysis tend to overcorrect for multiple substitutions and overestimate the ti/tv ratio, especially at low sequence divergence. The bi as, however, is not large enough to account for the observed patterns. Nucl eotide frequency biases, variation of substitution rates among sites, and d ifferent evolutionary dynamics at the three codon positions can be ruled ou t as possible causes. The likelihood-ratio test suggests that the ti/tv rat e ratios may be variable among evolutionary lineages. Without any biologica l evidence for such a variation, however. we are left with no plausible exp lanations for the observed patterns other than a possible saturation effect due to the unrealistic nature of the model assumed.