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Detecting recent selective sweeps while controlling for mutation rate and background selection

Christian D. Huber, Michael DeGiorgio, Ines Hellmann, Rasmus Nielsen
doi: https://doi.org/10.1101/018697
Christian D. Huber
1Max F. Perutz Laboratory, University of Vienna, Vienna, Austria
2Vienna Graduate School of Population Genetics, University of Veterinary Medicine, Vienna, Austria
3Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
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Michael DeGiorgio
4Departments of Biology and Statistics, Pennsylvania State University, University Park, PA, USA
5Institute for CyberScience, Pennsylvania State University, University Park, PA, USA
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Ines Hellmann
6Department Biologie II, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
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Rasmus Nielsen
7Departments of Integrative Biology and Statistics, University of California, Berkeley, CA, USA
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Abstract

A composite likelihood ratio test implemented in the program SweepFinder is a commonly used method for scanning a genome for recent selective sweeps. SweepFinder uses information on the spatial pattern of the site frequency spectrum (SFS) around the selected locus. To avoid confounding effects of background selection and variation in the mutation process along the genome, the method is typically applied only to sites that are variable within species. However, the power to detect and localize selective sweeps can be greatly improved if invariable sites are also included in the analysis. In the spirit of a Hudson-Kreitman-Aguadé test, we suggest to add fixed differences relative to an outgroup to account for variation in mutation rate, thereby facilitating more robust and powerful analyses. We also develop a method for including background selection modeled as a local reduction in the effective population size. Using simulations we show that these advances lead to a gain in power while maintaining robustness to mutation rate variation. Furthermore, the new method also provides more precise localization of the causative mutation than methods using the spatial pattern of segregating sites alone.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 30, 2015.
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Detecting recent selective sweeps while controlling for mutation rate and background selection
Christian D. Huber, Michael DeGiorgio, Ines Hellmann, Rasmus Nielsen
bioRxiv 018697; doi: https://doi.org/10.1101/018697
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Detecting recent selective sweeps while controlling for mutation rate and background selection
Christian D. Huber, Michael DeGiorgio, Ines Hellmann, Rasmus Nielsen
bioRxiv 018697; doi: https://doi.org/10.1101/018697

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