Estimating synonymous and nonsynonymous substitution rates |
| |
Authors: | Muse SV |
| |
Institution: | Department of Biology, Pennsylvania State University, University Park 16802, USA. |
| |
Abstract: | Partitioning the total substitution rate into synnonymous and nonsynonymous
components is a key aspect of many analyses in molecular evolution.
Numerous methods exist for estimating these rates. However, until recently
none of the estimation procedures were based on a sound statistical
footing. In this paper, the evolutionary model of Muse and Gaut (1994) is
used as the basis for two sets of parameters quantifying silent and
replacement substitution rates. The parameters are shown to be equal when
the four nucleotides are equally frequent and unequal otherwise.
Maximum-likelihood estimation of these parameters is described, and the
performance of these estimates is compared to that of existing estimation
procedures. It is shown that the estimates of Nei and Gojobori (1986) are
not unbiased for either set of parameters, although they provide very good
estimates for one set as long as sequence divergence is not too high.
However, some disturbing properties are found for the Nei and Gojobori
estimates. In particular, it is shown that the expected value of the Nei
and Gojobori estimate of silent substitution rate is a function of both the
silent and replacement substitution rates. The maximum-likelihood estimates
have no such problems.
|
| |
Keywords: | |
本文献已被 Oxford 等数据库收录! |
|