Rates of Synonymous Substitution and Base Composition f Nuclear Genes in Drosophila Etsuko

We compared the rates of synonymous (silent) substitution among various genes in a number of species of Drosophila. First, we found that even for a particular gene, the rate of synonymous substitution varied considerably with Drosophila lineages. Second, we showed a large variation in synonymous substitution rates among nuclear genes in Drosophila. These rates of synonymous substitution were correlated negatively with C content and positively with A content at the third codon positions. Nucleotide sequences were also compared between pseudogenes and their functional homologs. The C content of the pseudogenes was lower than that of the functional genes and the A content of the former was higher than that of the latter. Because the synonymous substitution for functional genes and the nucleotide substitution for pseudogenes are exempted from any selective constraint at the protein level, these observations could be explained by a biased pattern of mutation in the Drosophila nuclear genome. Such a bias in the mutation pattern may affect the molecular clock (local clock) of each nuclear gene of ach species. Finally, we obtained the average rates of synonymous substitution for three gene groups in Drosophila; 11.0 X lo-’, 17.5 X lo-’ and 27.1 X lO-’/site/year. A S the nucleotide sequence data for the Drosophila genome have accumulated, it has become apparent that most nuclear genes in Drosophila evolve at rates more than two times higher than those in rodents and other mammals (MORIYAMA 1987; CACCONE, AMATO and POWELL 1988; SHARP and LI 1989; ROWAN and HUNT 1991). Moreover, the rate of synonymous substitution of Drosophila genes is known to vary between genes (SHIELDS et a l . 1988; SHARP and LI 1989). The rate of nucleotide substitution can be affected by the mutation rate (KIMURA 1983), the generation time (or the number of replications), and the degree of selective constraints on the nucleotide sequence if the mutations are not selectively neutral (OHTA and TACHIDA 1990). One explanation for the higher rate of synonymous substitution in Drosophila is that it has a shorter generation time and, thus, more DNA replications per year than mammals (BRITTEN 1986; LI and TANIMURA 1987; KIMURA 1983, 1991). Differences in the accuracy of DNA replication or the efficiency of DNA repair are also possible explanations for the different rates of evolution between Drosophila and mammals. It is of interest that the characteristics of DNA polymerases in Drosophila may be different from those in mammals; DNA polymerase /3 in Drosophila is about twice as large as its mammalian counterpart and is detected only in the earlier stages of development (SAKAGUCHI and BOYD 1985), and the cryptic proofreading exonuclease activity of DNA polymerase a is unique for the embryo of Drosophila (WANG 199 1). Genetics 130 855-864 (April, 1992) SHIELDS et a l . (1988) have proposed a measure of biased usage of synonymous codons, “scaled x2.” Using this measure, they, as well as SHARP and LI (1 989), have shown that the rate of synonymous substitution in Drosophila is negatively correlated with the degree of codon usage bias. They have concluded that the variation in substitution rates among nuclear genes in Drosophila results from differences in the strengths of selective constraints on synonymous codons. Moreover, SHIELDS et a l . (1988) have pointed out that codon usage bias in the nuclear genome of Drosophila is associated with differences in the G + C content at synonymous sites. STARMER and SULLIVAN (1 989) also found shifts in nucleotide frequencies at the third codon positions by comparing the alcohol dehydrogenase (Adh) genes among various species of the subgenera Sophophora and Drosophila. For mammalian genes, TICHER and GRAUR (1989) reported that AT-rich genes accumulate more synonymous substitutions than GC-rich genes, and thus variation in synonymous substitution rates and unequal usage of codons must be due to negative selection against nucleotides A and T in synonymous sites. Further, WOLFE, SHARP and LI (1989) showed a correlation between the rate of synonymous substitution and the G + C content in a comparison of the nuclear genes of rat and mouse. For rodents, the G + C content of the GC-rich genes correlates negatively with substitution rates. On the other hand, that of AT-rich genes correlates positively with substitution rates. They suggested that variation in both synonymous substitution 856 E. N. Moriyama and T. Gojobori