Large Number of Replacement Polymorphisms in Rapidly Evolving Genes of Drosophila: Implications for Genome-Wide Surveys of DNA Polymorphism
Karl J. Schmida,c, Loredana Nigrob, Charles F. Aquadroc, and Diethard Tautz1,a
No evidence for a higher mutation rate:
It has been suggested that mutation rates may be variable in the genome of Drosophila. Interspecific DNA-DNA hybridization revealed a substantial fraction of single-copy DNA in the Drosophila genome that evolves rapidly (WERMAN et al. 1990 ). Sequencing of a boundary of fast and slowly evolving genomic regions led to the notion that the differences are not due to selection but to different mutation rates (MARTIN and MEYEROWITZ 1986 ). However, a high mutation rate is not supported as a plausible explanation for the rapid sequence divergence at the loci surveyed in this study. A high mutation rate should also affect silent sites of a locus and, consequently, a high silent substitution rate (in the absence of codon usage bias, which is the case at all three loci) would be expected. Compared to the silent divergence between D. melanogaster and D. simulans in the genes surveyed by MORIYAMA and POWELL 1996 , no larger numbers of silent substitutions per site are observed in interspecific comparisons of the three loci in this study (Table 7). Additionally, in our earlier screen (SCHMID and TAUTZ1997 ), 18 pairs of homologous sequences (including the three loci of this study) were compared between D. melanogaster and D. yakuba. Among all genes, the numbers of synonymous substitutions per site varied only 4- fold, while the numbers for replacement substitutions varied 30-fold. Since the number of silent substitutions per site is similar among all genes and is not correlated with the number of nonsynonymous substitutions, it is unlikely that the rapid evolution of these genes is driven by a high locus-specific mutation rate.