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MBE Advance Access published online on September 18, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl122
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted September 12, 2006

Letter

On the Varied Pattern of Evolution of Two Fungal Genomes: a Critique of Hughes and Friedman

Ziheng Yang 1 *

1 Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, England

* To whom correspondence should be addressed.
Ziheng Yang, E-mail: z.yang{at}ucl.ac.uk


  Abstract

A number of statistical tests have been proposed to detect positive Darwinian selection affecting a few amino acid sites in a protein, exemplified by an excess of nonsynonymous nucleotide substitutions. These tests are often more powerful than pairwise sequence comparison, which averages synonymous (dS) and nonsynonymous (dN) rates over the whole gene. In a recent study, however, Hughes and Friedman (2005: Mol. Biol. Evol. 22:1320-1324) argue that dS and dN are expected to fluctuate along the sequence by chance and that an excess of nonsynonymous differences in individual codons is no evidence for positive selection. The authors compared codons in protein-coding genes from the genomes of two yeast species, Saccharomyces cerevisiae and S. paradoxus. They calculated the proportions of synonymous and nonsynonymous differences per site (pS and pN) in every codon and discovered that pN is often greater than pS and that amongst some codons pS and pN are negatively correlated. The authors argued that these results invalidate previous tests of codons under positive selection. Here I discuss several errors of statistics in the analysis of Hughes and Friedman, including confusion of statistics with parameters, arbitrary data filtering, and derivation of hypotheses from data. I also apply likelihood ratio tests of positive selection to the yeast data and illustrate empirically that Hughes and Friedman's criticisms on such tests are not valid.

Keywords: genome evolution; likelihood ratio test; nonsynonymous substitution; positive selection; synonymous substitution.
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