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Genetics. Published Articles Ahead of Print: June 11, 2007, Copyright © 2007
doi:10.1534/genetics.106.069450

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

On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in non-equilibrium populations

Jeffrey D. Jensen 1*, Kevin R. Thornton 1, Carlos D. Bustamante 1 and Charles F. Aquadro 1

1 Cornell University

* To whom correspondence should be addressed. E-mail: jjensen{at}ucsd.edu.

Submitted on December 12, 2006
Revised on March 16, 2007
Accepted on 19 May 2007


  Abstract
A critically important challenge in empirical population genetics is distinguishing neutral non-equilibrium processes from selective forces that produce similar patterns of variation. We here examine the extent to which linkage disequilibrium (i.e., non-random associations between markers) improves this discrimination. We show that patterns of linkage disequilibrium recently proposed to be unique to hitchhiking models are replicated under non-equilibrium neutral models. We also demonstrate that jointly considering spatial patterns of association among variants alongside the site frequency spectrum is nonetheless of value. Through a comparison of models of equilibrium neutrality, non-equilibrium neutrality, equilibrium hitchhiking, non-equilibrium hitchhiking and recurrent hitchhiking, we evaluate an LD statistic ({omega}max) that appears to have power to identify regions recently shaped by positive selection. Most notably for experimental work, for the recently estimated bottleneck parameters for non-African populations of Drosophila melanogaster, we demonstrate that selected loci are distinguishable from neutral loci using this statistic.

Key Words: demography, linkage disequilibrium, recurrent hitchhiking, selective sweeps




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