Genomic Effects of Nucleotide Substitutions in Drosophila simulans

Genomic Effects of Nucleotide Substitutions in Drosophila simulans

Andrew D. Kern^a, Corbin D. Jones^a, and David J. Begun^a
^a Center for Population Biology, University of California, Davis, California 95616

Corresponding author: Andrew D. Kern, University of California, 1 Shields Ave., Davis, CA 95616., adkern{at}ucdavis.edu (E-mail)

Communicating editor: S. W. SCHAEFFER

Selective fixation of beneficial mutations reduces levels oflinked, neutral variation. The magnitude of this "hitchhikingeffect" is determined by the strength of selection and the recombinationrate between selected and neutral sites. Thus, depending onthe values of these parameters and the frequency with whichdirectional selection occurs, the genomic scale over which directionalselection reduces levels of linked variation may vary widely.Here we present a permutation-based analysis of nucleotide polymorphismsand fixations in Drosophila simulans. We show evidence of pervasivesmall-scale hitchhiking effects in this lineage. Furthermore,our results reveal that different types of fixations are associatedwith different levels of linked variation.

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