Molecular Biology and Evolution 17:975-978 (2000)
© 2000 Society for Molecular Biology and Evolution
Letter to the Editor |
Statistical Tests of Gamma-Distributed Rate Heterogeneity in Models of Sequence Evolution in Phylogenetics
,Department of Genetics, University of Cambridge, Cambridge, England
Likelihood ratio tests (LRTs) for comparing models of sequence evolution have become popular over the last few years (Goldman 1993
; Yang, Goldman and Friday 1994, 1995
; Huelsenbeck and Crandall 1997
; Huelsenbeck and Rannala 1997
). In their simplest form, such tests compare a simpler null hypothesis (H0) with a more complex alternative hypotheses (H1) which is a generalization of H0. H0 can be derived from H1 by fixing one or more of its free parameters at particular values, and the hypotheses are described as nested. Although it is also possible to test non-nested models (Goldman 1993
), nested models are often preferred, as statistical tests are simpler to perform and their results can be easier to interpret.
The test statistic for an LRT can be written as 2
= 2 ln(H1/H0) = 2(ln(H1) - ln(H0)), where H0 and H1 are the maximum-likelihood
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