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Originally published as Genetics Published Articles Ahead of Print on December 28, 2006.
Genetics, Vol. 175, 1395-1406, March 2007, Copyright © 2007
doi:10.1534/genetics.106.062828
The Structure of Linkage Disequilibrium Around a Selective Sweep
Gil McVean1
Department of Statistics, University of Oxford, Oxford OX1 3TG, United Kingdom
1 Address for correspondence: Department of Statistics, 1 S. Parks Rd., Oxford OX1 3TG, United Kingdom.
E-mail: mcvean{at}stats.ox.ac.uk
The fixation of advantageous mutations by natural selection has a profound impact on patterns of linked neutral variation. While it has long been appreciated that such selective sweeps influence the frequency spectrum of nearby polymorphism, it has only recently become clear that they also have dramatic effects on local linkage disequilibrium. By extending previous results on the relationship between genealogical structure and linkage disequilibrium, I obtain simple expressions for the influence of a selective sweep on patterns of allelic association. I show that sweeps can increase, decrease, or even eliminate linkage disequilibrium (LD) entirely depending on the relative position of the selected and neutral loci. I also show the importance of the age of the neutral mutations in predicting their degree of association and describe the consequences of such results for the interpretation of empirical data. In particular, I demonstrate that while selective sweeps can eliminate LD, they generate patterns of genetic variation very different from those expected from recombination hotspots.
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