Estimation of the Transition/Transversion Rate Bias and Species Sampling |
| |
Authors: | Ziheng Yang Anne D Yoder |
| |
Institution: | (1) Department of Biology (Galton Laboratory), University College London, 4 Stephenson Way, London NW1 2HE, England, GB;(2) Department of Cell and Molecular Biology, Northwestern University Medical School, Chicago, IL 60611, USA, US;(3) Department of Zoology, Field Museum of Natural History, Chicago, IL 60605, USA, US |
| |
Abstract: | The transition/transversion (ti/tv) rate ratios are estimated by pairwise sequence comparison and joint likelihood analysis
using mitochondrial cytochrome b genes of 28 primate species, representing both the Strepsirrhini (lemurs 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 multiple substitutions. The maximum-likelihood estimate of the ti/tv ratio changes
with the species included in the analysis. The ti/tv bias within the lemuriform taxa is found to be as strong as in the anthropoids,
in contradiction to an earlier study which sampled only one lemuriform. Simulations show the surprising result that both the
pairwise correction method and the joint likelihood analysis tend to overcorrect for multiple substitutions and overestimate
the ti/tv ratio, especially at low sequence divergence. The bias, however, is not large enough to account for the observed
patterns. Nucleotide frequency biases, variation of substitution rates among sites, and different evolutionary dynamics at
the three codon positions can be ruled out as possible causes. The likelihood-ratio test suggests that the ti/tv rate ratios
may be variable among evolutionary lineages. Without any biological evidence for such a variation, however, we are left with
no plausible explanations for the observed patterns other than a possible saturation effect due to the unrealistic nature
of the model assumed.
Received: 1 October 1997 / Accepted: 29 September 1998 |
| |
Keywords: | : Transition/transversion rate ratio — Maximum likelihood — Species sampling — Saturation — Lemurs — Primates |
本文献已被 PubMed SpringerLink 等数据库收录! |
|