MBE Advance Access published online on January 16, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn007
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Research Article |
Nonadaptive explanations for signatures of partial selective sweeps in Drosophila
* Department of Biological Sciences, Stanford University, Stanford, CA 94305
Department of Statistics, Stanford University, Stanford, CA 94305
Department of Human Genetics, University of Michigan, Ann Arbor, MI, 98109
Department of Ecology & Evolutionary Biology, University of Colorado at Boulder, Boulder, CO 80309
Corresponding author: J. Michael Macpherson, Department of Biological Sciences, Stanford University, Stanford, CA, 94305, Phone +1 650 736 4952, Fax +1 650 723 6132, macpher{at}stanford.edu
Received for publication August 9, 2007. Revision received November 25, 2007. Accepted for publication January 1, 2008.
A beneficial mutation which has nearly but not yet fixed in a population produces a characteristic haplotype configuration, called a partial selective sweep. Whether non-adaptive processes might generate similar haplotype configurations has not been previously explored. Here we consider five population genetic datasets taken from regions flanking high frequency transposable elements in North American strains of D. 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. Where most of the datasets would be rejected as non-neutral under the standard neutral null model, only the dataset for which there is strong external evidence in support of an adaptive transposition appears to be non-neutral 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