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Originally published as Genetics Published Articles Ahead of Print on February 1, 2006.
Genetics, Vol. 172, 2647-2663, April 2006, Copyright © 2006
doi:10.1534/genetics.105.050179
The Hitchhiking Effect on Linkage Disequilibrium Between Linked Neutral Loci
Wolfgang Stephan*,1,
Yun S. Song
and
Charles H. Langley
* Section of Evolutionary Biology, Biocenter, University of Munich, 82152 Planegg-Martinsried, Germany and Department of Computer Sciences and Section of Evolution and Ecology, University of California, Davis, California 95616
1 Corresponding author: University of Munich, Grosshaderner Strasse 2, 82152 Planegg, Germany.
E-mail: stephan{at}zi.biologie.uni-muenchen.de
We analyzed a three-locus model of genetic hitchhiking with one locus experiencing positive directional selection and two partially linked neutral loci. Following the original hitchhiking approach by Maynard Smith and Haigh, our analysis is purely deterministic. In the first half of the selected phase after a favored mutation has entered the population, hitchhiking may lead to a strong increase of linkage disequilibrium (LD) between the two neutral sites if both are <0.1s away from the selected site (where s is the selection coefficient). In the second half of the selected phase, the main effect of hitchhiking is to destroy LD. This occurs very quickly (before the end of the selected phase) when the selected site is between both neutral loci. This pattern cannot be attributed to the well-known variation-reducing effect of hitchhiking but is a consequence of secondary hitchhiking effects on the recombinants created in the selected phase. When the selected site is outside the neutral loci (which are, say, <0.1s apart), however, a fast decay of LD is observed only if the selected site is in the immediate neighborhood of one of the neutral sites (i.e., if the recombination rate r between the selected site and one of the neutral sites satisfies 
). If the selected site is far away from the neutral sites (say, r > 0.3s), the decay rate of LD approaches that of neutrality. Averaging over a uniform distribution of initial gamete frequencies shows that the expected LD at the end of the hitchhiking phase is driven toward zero, while the variance is increased when the selected site is well outside the two neutral sites. When the direction of LD is polarized with respect to the more common allele at each neutral site, hitchhiking creates more positive than negative linkage disequilibrium. Thus, hitchhiking may have a distinctively patterned LD-reducing effect, in particular near the target of selection.
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