Skip to main content
Journal cover image

Estimation of the transition/transversion rate bias and species sampling.

Publication ,  Journal Article
Yang, Z; Yoder, AD
Published in: Journal of molecular evolution
March 1999

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.

Duke Scholars

Published In

Journal of molecular evolution

DOI

EISSN

1432-1432

ISSN

0022-2844

Publication Date

March 1999

Volume

48

Issue

3

Start / End Page

274 / 283

Related Subject Headings

  • Species Specificity
  • Primates
  • Models, Genetic
  • Likelihood Functions
  • Lemur
  • Humans
  • Evolutionary Biology
  • Cytochrome b Group
  • Animals
  • Algorithms
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Yang, Z., & Yoder, A. D. (1999). Estimation of the transition/transversion rate bias and species sampling. Journal of Molecular Evolution, 48(3), 274–283. https://doi.org/10.1007/pl00006470
Yang, Z., and A. D. Yoder. “Estimation of the transition/transversion rate bias and species sampling.Journal of Molecular Evolution 48, no. 3 (March 1999): 274–83. https://doi.org/10.1007/pl00006470.
Yang Z, Yoder AD. Estimation of the transition/transversion rate bias and species sampling. Journal of molecular evolution. 1999 Mar;48(3):274–83.
Yang, Z., and A. D. Yoder. “Estimation of the transition/transversion rate bias and species sampling.Journal of Molecular Evolution, vol. 48, no. 3, Mar. 1999, pp. 274–83. Epmc, doi:10.1007/pl00006470.
Yang Z, Yoder AD. Estimation of the transition/transversion rate bias and species sampling. Journal of molecular evolution. 1999 Mar;48(3):274–283.
Journal cover image

Published In

Journal of molecular evolution

DOI

EISSN

1432-1432

ISSN

0022-2844

Publication Date

March 1999

Volume

48

Issue

3

Start / End Page

274 / 283

Related Subject Headings

  • Species Specificity
  • Primates
  • Models, Genetic
  • Likelihood Functions
  • Lemur
  • Humans
  • Evolutionary Biology
  • Cytochrome b Group
  • Animals
  • Algorithms