Yang Z, Goldman N
Department of Animal Sciences, Beijing Agricultural University.
Yi Chuan Xue Bao. 1994;21(1):17-23.
Markov process models of nucleotide substitution are evaluated. A model proposed by Lanave et al (1984), alleged to need no priori assumption about the substitution pattern, is found to have the assumption of reversibility. Calculations based on the 2-p, 4-p, and 6-p substitution schemes show that site variation of substitution speed leads to serious under-estimation of sequence divergence by various methods. Spatial pattern variation also leads to under-estimation, but the discrepancy is slight. A nonhomogeneous Markov process model is used to study the temporal variations of rates and it is shown that the estimated number of substitutions reflects a rate averaged over time. The implications of those results to evolutionary phylogenetics are discussed.
对核苷酸替换的马尔可夫过程模型进行了评估。发现Lanave等人（1984年）提出的一个模型，据称无需对替换模式进行先验假设，却存在可逆性假设。基于二核苷酸、四核苷酸和六核苷酸替换方案的计算表明，替换速度的位点变化会导致各种方法严重低估序列分歧。空间模式变化也会导致低估，但差异较小。使用非齐次马尔可夫过程模型来研究速率的时间变化，结果表明估计的替换数反映了随时间平均的速率。讨论了这些结果对进化系统发育学的影响。
