title: Variation in the pattern of synonymous and nonsynonymous difference between two fungal genomes.
abstract: The proportion of synonymous nucleotide differences per synonymous site (p(S)) and the proportion of nonsynonymous differences per nonsynonymous site (p(N)) 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 p(N) > p(S) were observed than expected, based on random pairing of observed p(S) and p(N) 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 p(N) > p(S) were characterized not only by unusually high p(N) but also by unusually low p(S). On the other hand, the number of codons with p(N)>p(S) (where p(S) is the mean p(S) for all codons) was very similar to the random expectation, and the observed number of 30-codon windows with p(N) > p(S) was significantly lower than the random expectation. These results imply that the occurrence of a certain number of codons or codon windows with p(N) > p(S) is expected given the nature of nucleotide substitution and need not imply the action of positive Darwinian selection.
authors.affiliation: Department of Biological Sciences, University of South Carolina, USA.
authors.forename: Austin L
authors.initials: AL
authors.lastname: Hughes
authors.forename: Robert
authors.initials: R
authors.lastname: Friedman
mesh_terms: D003062:Codon / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics*; D016681:Genome, Fungal; D008957:Models, Genetic; D009154:Mutation; D012440:Saccharomyces / Q000145:classification* / Q000235:genetics*; D012641:Selection, Genetic
chemical_list: D003062:Codon