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MBE Advance Access originally published online on September 29, 2004
Molecular Biology and Evolution 2005 22(1):51-62; doi:10.1093/molbev/msh269
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Molecular Biology and Evolution vol. 22 no. 1 © Society for Molecular Biology and Evolution 2005; all rights reserved.

Research Article

Patterns of Polymorphism and Divergence from Noncoding Sequences of Drosophila melanogaster and D. simulans: Evidence for Nonequilibrium Processes

Andrew D. Kern and David J. Begun

Center for Population Biology, University of California, Davis

E-mail: adkern{at}ucdavis.edu.

Despite the fact that D. melanogaster and D. simulans have been the central model system for molecular population genetics, few data are available for noncoding regions. Here, we present an analysis of population genetic data from intergenic regions and comparisons of these data to previously collected data from introns and exons. Polymorphisms and fixations were categorized as A/T to G/C or G/C to A/T changes and were polarized by inferring the ancestral state using both parsimony and maximum likelihood. Noncoding fixations in both D. melanogaster and D. simulans were consistent with equilibrium base-composition evolution. However, polarized noncoding polymorphisms, revealed a different pattern. Although A/T to G/C and G/C to A/T polymorphisms in D. simulans were consistent with equilibrium, we observed a highly significant dearth of A/T to G/C polymorphisms in D. melanogaster introns but not in intergenic sequences. Such data could be explained by recent evolution of mutational biases associated with transcription or by lineage-specific selection on base composition. These data reveal the complexity of evolutionary processes acting even on noncoding DNA in Drosophila.

Key Words: Drosophila • polymorphism • divergence • noncoding DNA • base composition • introns


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