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

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dc.contributor.authorHuber, C.D.
dc.contributor.authorDeGiorgio, M.
dc.contributor.authorHellmann, I.
dc.contributor.authorNielsen, R.
dc.date.issued2016
dc.description.abstractA 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 (along the chromosome) of the site frequency spectrum 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 adding fixed differences relative to an out‐group to account for variation in mutation rate, thereby facilitating more robust and powerful analyses. We also develop a method for including background selection, modelled 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.
dc.description.statementofresponsibilityChristian D. Huber, Michael DeGiorgio, Ines Hellmann, Rasmus Nielsen
dc.identifier.citationMolecular Ecology, 2016; 25(1):142-156
dc.identifier.doi10.1111/mec.13351
dc.identifier.issn0962-1083
dc.identifier.issn1365-294X
dc.identifier.orcidHuber, C.D. [0000-0002-2267-2604]
dc.identifier.urihttp://hdl.handle.net/2440/116424
dc.language.isoen
dc.publisherWiley
dc.rights© 2015 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
dc.source.urihttps://doi.org/10.1111/mec.13351
dc.subjectBackground selection; Hudson–Kreitman–Aguadé test; population bottlenecks; sweep detection
dc.titleDetecting recent selective sweeps while controlling for mutation rate and background selection
dc.typeJournal article
pubs.publication-statusPublished

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