MBE Advance Access published online on May 29, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn125
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Research Article |
Positive and negative selection on noncoding DNA in Drosophila simulans
1 Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh
2 Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego
3 Department of Ecology and Evolutionary Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University
* Correspondence: Penelope R. Haddrill, Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, King's Buildings, Edinburgh EH9 3JT, Phone: (+44) 131 650 5543, Fax: (+44) 131 650 6564. Email: p.haddrill{at}ed.ac.uk.
Received for publication March 31, 2008. Revision received May 16, 2008. Accepted for publication May 20, 2008.
There is now a wealth of evidence that some of the most important regions of the genome are found outside those that encode proteins, and noncoding regions of the genome have been shown to be subject to substantial levels of selective constraint, particularly in Drosophila. Recent work has suggested that these regions may also have been subject to the action of positive selection, with large fractions of noncoding divergence having been driven to fixation by adaptive evolution. However, this work has focussed on Drosophila melanogaster, which is thought to have experienced a reduction in effective population size (Ne), and thus a reduction in the efficacy of selection, compared to its closest relative Drosophila simulans. Here, we examine patterns of evolution at several classes of noncoding DNA in D. simulans, and find that all noncoding DNA is subject to the action of negative selection, indicated by reduced levels of polymorphism and divergence, and a skew in the frequency spectrum towards rare variants. We find that the signature of negative selection on noncoding DNA and nonsynonymous sites is obscured to some extent by purifying selection acting on preferred to unpreferred synonymous codon mutations. We investigate the extent to which divergence in noncoding DNA is inferred to be the product of positive selection and to what extent these inferences depend on selection on synonymous sites and demography. Based on patterns of polymorphism and divergence for different classes of synonymous substitution, we find the divergence excess inferred in noncoding DNA and nonsynonymous sites in the D. simulans lineage difficult to reconcile with demographic explanations.
Key Words: Drosophila simulans • noncoding DNA • natural selection • adaptive evolution • McDonald-Kreitman test • codon usage bias
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