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

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 (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 p

SUBMITTER: Huber CD 

PROVIDER: S-EPMC5082542 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature