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Genetics. Published Articles Ahead of Print: December 28, 2006, Copyright © 2006
doi:10.1534/genetics.106.062828

A more recent version of this article appeared on March 1, 2007.
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REGULAR RESEARCH PAPERS

The structure of linkage disequilibrium around a selective sweep

Gil McVean 1*

1 University of Oxford

* To whom correspondence should be addressed. E-mail: mcvean{at}stats.ox.ac.uk.

Submitted on June 30, 2006
Revised on September 20, 2006
Accepted on 24 December 2006


  Abstract
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 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.

Key Words: Coalescent, Linkage disequilibrium, Recombination hotspot, Selective sweep




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