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MBE Advance Access published online on August 25, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh242
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted August 18, 2004

Research Article

Comparison of Three Methods for Estimating Rates of Synonymous and Non-synonymous Nucleotide Substitutions

Yun-Huei Tzeng 1, Runsun Pan 2, Wen-Hsiung Li 3*

1 Department of Ecology and Evolution, University of Chicago, Chicago, USA; Department of Mathematics, National Tsing Hua University, Hsinchu, Taiwan
2 Department of Ecology and Evolution, University of Chicago, Chicago, USA; Institute of Information Science, Academia Sinica, Taiwan
3 Department of Ecology and Evolution, University of Chicago, Chicago, USA

* To whom correspondence should be addressed. E-mail: whli{at}uchicago.edu.


  Abstract

Three frequently used methods for estimating the synonymous and nonsynonymous substitution rates (Ks and Ka) -- Li-Wu-Luo (1985), Li (1993) and Pamilo and Bianchi (1993), and Goldman and Yang (1994) as in the package PAML - were evaluated and compared for their accuracies; these methods are denoted by LWL85, LPB93, and GY94, respectively. For this purpose we used a codon evolution model to obtain the expected Ka and Ks values for the above three methods and compared the values with those obtained by the three methods. We also proposed some modifications of LWL85 and LPB93 to increase their accuracies. Our computer simulations under the codon evolution model showed that for sequences ≤ 300 codons the performance of GY94 may not be reliable. For longer sequences, GY94 is more accurate for estimating the Ka/Ks ratio than the modified LPB93 and LWL85 in the majority of the cases studied. This is particularly so when k ≥ 3, which is the transition/transversion (mutation) rate ratio. However, when k is ~2 and when the sequence divergence is relatively large, the modified LWL85 performed better than GY94 and the modified LPB93. The inferiority of LPB93 to LWL85 is surprising because LPB93 was intended to improve LWL85. Also, it has been thought that the codon-based method of GY94 is better than the heuristic method of LWL85, but our simulation results showed that in many cases the opposite was true, even though our simulation was based on the codon evolution model.

Keywords: synonymous substitution; nonsynonymous substitution; estimation methods; Ka/Ks ratio; accuracy of estimation.
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