MBE Advance Access originally published online on March 2, 2005
Molecular Biology and Evolution 2005 22(5):1320-1324; doi:10.1093/molbev/msi120
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Research Article |
Variation in the Pattern of Synonymous and Nonsynonymous Difference Between Two Fungal Genomes
Department of Biological Sciences, University of South Carolina
E-mail: austin{at}biol.sc.edu.
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 Saccharomyces 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 
(where pS is the mean 
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.
Key Words: genome evolution • nonsynonymous substitution • positive selection • synonymous substitution
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