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MBE Advance Access published online on September 29, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh269
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted August 30, 2004

Research Article

Patterns of Polymorphism and Divergence from Non-coding Sequences of D. melanogaster and D. simulans: Evidence for Non-equilibrium Processes

Andrew D. Kern 1* and David J. Begun 1

1 Center for Population Biology, University of California, Davis, One Shields Ave, Davis, CA 95616

* To whom correspondence should be addressed. E-mail: adkern{at}ucdavis.edu.


  Abstract

Despite the fact that D. melanogaster and D. simulans have been the central model system for molecular population genetics, few data are available for non-coding 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. Non-coding fixations in both D. melanogaster and D. simulans were consistent with equilibrium base composition evolution. However, polarized non-coding polymorphisms, revealed a different pattern. While 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 intergenic sequence. 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 non-coding DNA in Drosophila.

Keywords: Drosophila; Polymorphism; Divergence; non-coding DNA; Base Composition; Introns.
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