GC-biased segregation of noncoding polymorphisms in Drosophila.

The study of base composition evolution in Drosophila has been achieved mostly through the analysis of coding sequences. Third codon position GC content, however, is influenced by both neutral forces (e.g., mutation bias) and natural selection for codon usage optimization. In this article, large data sets of noncoding DNA sequence polymorphism in D. melanogaster and D. simulans were gathered from public databases to try to disentangle these two factors-noncoding sequences are not affected by selection for codon usage. Allele frequency analyses revealed an asymmetric pattern of AT vs. GC noncoding polymorphisms: AT --> GC mutations are less numerous, and tend to segregate at a higher frequency, than GC --> AT ones, especially at GC-rich loci. This is indicative of nonstationary evolution of base composition and/or of GC-biased allele transmission. Fitting population genetics models to the allele frequency spectra confirmed this result and favored the hypothesis of a biased transmission. These results, together with previous reports, suggest that GC-biased gene conversion has influenced base composition evolution in Drosophila and explain the correlation between intron and exon GC content.