Originally published as Genetics Published Articles Ahead of Print on September 12, 2005.

Genetics, Vol. 172, 221-228, January 2006, Copyright © 2006
doi:10.1534/genetics.105.046524

GC-Biased Segregation of Noncoding Polymorphisms in Drosophila

Nicolas Galtier¹, Eric Bazin and Nicolas Bierne

UMR 5171, "Génome, Populations, Interactions, Adaptation," CNRS, Université Montpellier 2, IFREMER, 34095 Montpellier, France

¹ Corresponding author: CNRS UMR 5171—"Génome, Populations, Interactions, Adaptation," Université Montpellier 2, CC 063, Place E. Bataillon, 34095 Montpellier, France.
E-mail: galtier{at}univ-montp2.fr

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.

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