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MBE Advance Access published online on March 2, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msi120
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© The Author 2005. 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@oupjournals.org
Accepted February 21, 2005

Research Article

Variation in the Pattern of Synonymous and Nonsynonymous Difference between Two Fungal Genomes

Austin L. Hughes 1* and Robert Friedman 1

1 Department of Biological Sciences, University of South Carolina, Columbia SC 29205 USA

* To whom correspondence should be addressed.
Austin L. Hughes, E-mail: austin{at}biol.sc.edu


  Abstract

The proportion of synonymous nucleotide differences per synonymous site (pS) and the proportion of nonsynonymous differences per nonsynonymous site (pN) were computed at 1,993,217 individual codons in 4,133 protein-coding genes between the two yeast species Saccharomyces cerevisiae and S. paradoxus. When the modified Nei-Gojobori method was used, significantly more codons with pN > pS were observed than expected based on random pairing of observed pS and pN values. However, this finding was most likely explained by the presence of a strong negative correlation between the number of synonymous differences and the number of nonsynonymous differences at codons with at least one difference. As a result of this correlation, codons with pN > pS were characterized not only by unusually high pN but also by unusually low pS. On the other hand, the number of codons with pN > pS{overline} (where pS is the mean pS{overline} for all codons) was very similar to the random expectation; and the observed number of 30-codon windows with pN > pS was significantly lower than the random expectation. These results imply that the occurrence of a certain number of codons or codon windows with pN > pS is expected given the nature of nucleotide substitution and need not imply the action of positive Darwinian selection.


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