Gu X, Li W H
Institute of Molecular Evolutionary Genetics, 328 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802, USA.
Proc Natl Acad Sci U S A. 1998 May 26;95(11):5899-905. doi: 10.1073/pnas.95.11.5899.
Estimation of evolutionary distances has always been a major issue in the study of molecular evolution because evolutionary distances are required for estimating the rate of evolution in a gene, the divergence dates between genes or organisms, and the relationships among genes or organisms. Other closely related issues are the estimation of the pattern of nucleotide substitution, the estimation of the degree of rate variation among sites in a DNA sequence, and statistical testing of the molecular clock hypothesis. Mathematical treatments of these problems are considerably simplified by the assumption of a stationary process in which the nucleotide compositions of the sequences under study have remained approximately constant over time, and there now exist fairly extensive studies of stationary models of nucleotide substitution, although some problems remain to be solved. Nonstationary models are much more complex, but significant progress has been recently made by the development of the paralinear and LogDet distances. This paper reviews recent studies on the above issues and reports results on correcting the estimation bias of evolutionary distances, the estimation of the pattern of nucleotide substitution, and the estimation of rate variation among the sites in a sequence.
进化距离的估计一直是分子进化研究中的一个主要问题，因为估计基因的进化速率、基因或生物体之间的分歧日期以及基因或生物体之间的关系都需要进化距离。其他密切相关的问题包括核苷酸替换模式的估计、DNA序列中位点间速率变化程度的估计以及分子钟假说的统计检验。通过假设一个平稳过程，这些问题的数学处理得到了极大简化，在该过程中，所研究序列的核苷酸组成随时间保持近似恒定，并且目前存在对核苷酸替换平稳模型的相当广泛的研究，尽管仍有一些问题有待解决。非平稳模型要复杂得多，但最近通过平行线性距离和对数行列式距离的发展取得了显著进展。本文综述了关于上述问题的近期研究，并报告了关于校正进化距离估计偏差、核苷酸替换模式估计以及序列中位点间速率变化估计的结果。
