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Summary: Accuracy and Power of the Likelihood Ratio Test for Comparing Evolutionary
Rates Among Genes
Jan Erik Aagaard, Patrick Phillips
Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, OR 97403, USA
Received: 29 April 2004 / Accepted: 11 October 2004 [Reviewing Editor: Dr. Rosmus Nielsen]
Abstract. Sequences for multiple protein-coding
genes are now commonly available from several, of-
ten closely related species. These data sets offer
intriguing opportunities to test hypotheses regarding
whether different types of genes evolve under differ-
ent selective pressures. Although maximum likeli-
hood (ML) models of codon substitution that are
suitable for such analyses have been developed, little
is known about the statistical properties of these tests.
We use a previously developed fixed-sites model and
computer simulations to examine the accuracy and
power of the likelihood ratio test (LRT) in comparing
the nonsynonymous-to-synonymous substitution rate
ratio (x = dN/dS) between two genes. Our results
show that the LRT applied to fixed-sites models may
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