Divergence at “Silent” Sites in Drosophila DNA

Patterns of codon usage and “silent” DNA divergence suggest that natural selection discriminates among synonymous codons in Drosophila. “Preferred” codons are consistently found in higher frequencies within their synonymous families in Drosophila melanogaster genes. This suggests a simple model of silent DNA evolution where natural selection favors mutations from unpreferred to preferred codons (preferred changes). Changes in the opposite direction, from preferred to unpreferred synonymous codons (unpreferred changes), are selected against. Here, selection on synonymous DNA mutations is investigated by comparing the evolutionary dynamics of these two categories of silent DNA changes. Sequences from outgroups are used to determine the direction of synonymous DNA changes within and between D. melanogaster and Drosophila simulans for five genes. Population genetics theory shows that differences in the fitness effect of mutations can be inferred from the comparison of ratios of polymorphism to divergence. Unpreferred changes show a significantly higher ratio of polymorphism to divergence than preferred changes in the D. simulans lineage, confirming the action of selection at silent sites. An excess of unpreferred fixations in 28 genes suggests a relaxation of selection on synonymous mutations in D. metunoguster. Estimates of selection coefficients for synonymous mutations (3.6 < 1 Ngl < 1.3) in D. simulans are consistent with the reduced efficacy of natural selection ( I NgI < 1 ) in the threeto sixfold smaller effective population size of D. melanoguster. Synonymous DNA changes appear to be a prevalent class of weakly selected mutations in Drosophila. T HE strongest evidence for natural selection at “silent” sites in DNA comes from studies of codon usage in Escherichia coli and Saccharomyces cerevisiae. In these species, synonymous codon usage is biased toward a subset of preferred codons, which generally code for the most abundant tRNA( s) for each amino acid ( IKEMURA 1981; BENNETZEN and HALL 1982; GROSJEAN and FREIRS 1982). The degree to which codon usage is biased varies considerably between genes and correlates strongly with gene expression levels ( IKEMURA 1985). Silent DNA divergence between E. coli and Salmonella typhemun’um is inversely related to codon usage bias, which suggests the action of purifymg selection at preferred codons (SHARP and LI 1987). These patterns, termed “major codon preference,” are consistent with natural selection discriminating among synonymous codons to enhance translational efficiency and/or accuracy ( BULMER 1991 ) . Patterns of codon usage and silent DNA evolution in D. melanogaster are similar to those found in E. coli and yeast (SHIELDS et al. 1988). Codon usage is biased toward a subset of (mostly G/C-ending) synonymous codons for each amino acid. Relative tRNA abundances have been quantified for only a few amino acids, and, where the data exist, codon preferences correlate with Author e-mail: akas&midway.uchicago.edu Genetics 139 1067-1076 (February. 1995) the abundant tRNA (see SHIELDS et al. 1988). Although relative expression levels are difficult to quantify in multicellular organisms, where gene expression can be tissueand developmental-stage specific, highly expressed loci such as ribosomal protein genes and Adh show highly biased codon usage, whereas less highly expressed genes such as Adhr show more equal usage among synonymous codons. Silent DNA divergence between Drosophila species is inversely related to codon usage bias, which again suggests varylng levels of purifying selection at different loci (SHARP and LI 1989; CARULLI et al. 1993). Two observations add further support for the role of selection at silent sites in Drosophila. Evidence for lower codon usage bias in regions of low recombination in the D. melanogastergenome is consistent with theoretical predictions of the reduced efficacy of selection in such regions ( KLIMAN and HEY 1993a). An association between codon bias and functional constraint at the protein level has been found in Drosophila, suggesting that natural selection discriminates among synonymous codons to enhance the accuracy of protein synthesis Major codon preference can be modeled under a simple form of selection-mutation-drift at silent sites (SHARP and L1 1986; BULMER 1991). Selection favors a subset of synonymous codons for each amino acid, (AKASHI 1994).