Estimation of evolutionary distances under stationary and nonstationary models of nucleotide substitution
- Xun Gu* and
- Wen-Hsiung Li†,‡
Abstract
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.
Footnotes
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↵ ‡ To whom reprint requests should be addressed. e-mail: li{at}hgc.sph.tmc.uth.edu.
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This paper was presented at the colloquium “Computational Biomolecular Science,” organized by Russell Doolittle, J. Andrew McCammon, and Peter G. Wolynes, held September 11–13, 1997, sponsored by the National Academy of Sciences at the Arnold and Mabel Beckman Center in Irvine, CA.
- ABBREVIATIONS:
- SR,
- stationary time reversible;
- SRV,
- SR rate-variable;
- NR,
- time-irreversible;
- TR,
- time-reversible
- Copyright © 1998, The National Academy of Sciences
