- THIS ARTICLE
- Full Text
- Full Text (PDF)
-
All Versions of this Article:
genetics.106.069450v1
176/4/2371 most recent - Alert me when this article is cited
- Alert me if a correction is posted
- SERVICES
- Similar articles in this journal
- Similar articles in PubMed
- Alert me to new issues of the journal
- Download to citation manager
- Reprints & Permissions
- CITING ARTICLES
- Citing Articles via HighWire
- Citing Articles via Google Scholar
- GOOGLE SCHOLAR
- Articles by Jensen, J. D.
- Articles by Aquadro, C. F.
- Search for Related Content
- PUBMED
- PubMed Citation
- Articles by Jensen, J. D.
- Articles by Aquadro, C. F.
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
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
and
Charles F. Aquadro*
* Department of Molecular Biology and Genetics and 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 (
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:
 |
|
 |
|
  P. Pfaffelhuber, A. Lehnert, and W. Stephan Linkage Disequilibrium Under Genetic Hitchhiking in Finite Populations Genetics, May 1, 2008; 179(1): 527 - 537. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 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]
|
|
|
|
|
|
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]
|
|