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MBE Advance Access originally published online on January 16, 2008
Molecular Biology and Evolution 2008 25(6):1025-1042; doi:10.1093/molbev/msn007
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© The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Articles

Nonadaptive Explanations for Signatures of Partial Selective Sweeps in Drosophila

J. Michael Macpherson*, Josefa González*, Daniela M. Witten{dagger}, Jerel C. Davis*, Noah A. Rosenberg{ddagger}, Aaron E. Hirsh§ and Dmitri A. Petrov*

* Department of Biological Sciences, Stanford University
{dagger} Department of Statistics, Stanford University
{ddagger} Department of Human Genetics, University of Michigan, Ann Arbor
§ Department of Ecology & Evolutionary Biology, University of Colorado at Boulder

E-mail: macpher{at}stanford.edu

Accepted for publication January 1, 2008.

A beneficial mutation that has nearly but not yet fixed in a population produces a characteristic haplotype configuration, called a partial selective sweep. Whether nonadaptive processes might generate similar haplotype configurations has not been extensively explored. Here, we consider 5 population genetic data sets taken from regions flanking high-frequency transposable elements in North American strains of Drosophila melanogaster, each of which appears to be consistent with the expectations of a partial selective sweep. We use coalescent simulations to explore whether incorporation of the species' demographic history, purifying selection against the element, or suppression of recombination caused by the element could generate putatively adaptive haplotype configurations. Whereas most of the data sets would be rejected as nonneutral under the standard neutral null model, only the data set for which there is strong external evidence in support of an adaptive transposition appears to be nonneutral under the more complex null model and in particular when demography is taken into account. High-frequency, derived mutations from a recently bottlenecked population, such as we study here, are of great interest to evolutionary genetics in the context of scans for adaptive events; we discuss the broader implications of our findings in this context.

Key Words: bottleneck • transposable element • coalescent simulation • partial selective sweep

Marcy Uyenoyama, Associate Editor


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