help button home button Genetics J Histo Cito
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Originally published as Genetics Published Articles Ahead of Print on June 11, 2007.

Genetics, Vol. 176, 2371-2379, August 2007, Copyright © 2007
doi:10.1534/genetics.106.069450

This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow All Versions of this Article:
genetics.106.069450v1
176/4/2371    most recent
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Jensen, J. D.
Right arrow Articles by Aquadro, C. F.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Jensen, J. D.
Right arrow Articles by Aquadro, C. F.

On the Utility of Linkage Disequilibrium as a Statistic for Identifying Targets of Positive Selection in Nonequilibrium Populations

Jeffrey D. Jensen*,1, Kevin R. Thornton*,2, Carlos D. Bustamante{dagger} and Charles F. Aquadro*

* Department of Molecular Biology and Genetics and {dagger} Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853

1 Corresponding author: Section of Ecology, Behavior and Evolution, AP&M 4th Floor Annex, University of California, La Jolla, California 92037.
E-mail: jjensen{at}ucsd.edu

A critically important challenge in empirical population genetics is distinguishing neutral nonequilibrium processes from selective forces that produce similar patterns of variation. We here examine the extent to which linkage disequilibrium (i.e., nonrandom associations between markers) improves this discrimination. We show that patterns of linkage disequilibrium recently proposed to be unique to hitchhiking models are replicated under nonequilibrium 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, nonequilibrium neutrality, equilibrium hitchhiking, nonequilibrium hitchhiking, and recurrent hitchhiking, we evaluate a linkage disequilibrium (LD) statistic ({omega}max) that appears to have power to identify regions recently shaped by positive selection. Most notably, for demographic parameters relevant to non-African populations of Drosophila melanogaster, we demonstrate that selected loci are distinguishable from neutral loci using this statistic.




This article has been cited by other articles:


Home page
 Genome Res.Home page
P. Andolfatto
Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome
Genome Res., December 1, 2007; 17(12): 1755 - 1762.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
J. D. Jensen, V. L. Bauer DuMont, A. B. Ashmore, A. Gutierrez, and C. F. Aquadro
Patterns of Sequence Variability and Divergence at the diminutive Gene Region of Drosophila melanogaster: Complex Patterns Suggest an Ancestral Selective Sweep
Genetics, October 1, 2007; 177(2): 1071 - 1085.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Copyright © 2007 by the Genetics Society of America.