Comparison of three methods for estimating rates of synonymous and nonsynonymous nucleotide substitutions

Three frequently used methods for estimating the synonymous and nonsynonymous substitution rates (Ks and Ka) 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 less than or equal to300 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 greater than or equal to 3, which is the transition/transversion (mutation) rate ratio. However, when k is approximately 2 and when the sequence divergence is relatively large, the modified LWL85 performed better than GY94 and the modified LP1393. 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.