- THIS ARTICLE
- Full Text
- Full Text (PDF)
- Data Supplement
-
All Versions of this Article:
genetics.106.061432v1
174/3/1431 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 Zeng, K.
- Articles by Wu, C.-I
- Search for Related Content
- PUBMED
- PubMed Citation
- Articles by Zeng, K.
- Articles by Wu, C.-I
Originally published as Genetics Published Articles Ahead of Print on September 1, 2006.
Genetics, Vol. 174, 1431-1439, November 2006, Copyright © 2006
doi:10.1534/genetics.106.061432
Statistical Tests for Detecting Positive Selection by Utilizing High-Frequency Variants
Kai Zeng*,
,1,
Yun-Xin Fu
,
,
Suhua Shi* and
Chung-I Wu
* State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou 510275, China, Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, Human Genetics Center, School of Public Health, University of Texas, Houston, Texas 77030 and Laboratory for Conservation and Utilization of Bioresources, Yunnan University, Kunming 650091, China
1 Corresponding author: 1101 E. 57th St., Chicago, IL 60637.
E-mail: kzeng{at}uchicago.edu
By comparing the low-, intermediate-, and high-frequency parts of the frequency spectrum, we gain information on the evolutionary forces that influence the pattern of polymorphism in population samples. We emphasize the high-frequency variants on which positive selection and negative (background) selection exhibit different effects. We propose a new estimator of 
(the product of effective population size and neutral mutation rate), L, which is sensitive to the changes in high-frequency variants. The new L allows us to revise Fay and Wu's H-test by normalization. To complement the existing statistics (the H-test and Tajima's D-test), we propose a new test, E, which relies on the difference between L and Watterson's W. We show that this test is most powerful in detecting the recovery phase after the loss of genetic diversity, which includes the postselective sweep phase. The sensitivities of these tests to (or robustness against) background selection and demographic changes are also considered. Overall, D and H in combination can be most effective in detecting positive selection while being insensitive to other perturbations. We thus propose a joint test, referred to as the DH test. Simulations indicate that DH is indeed sensitive primarily to directional selection and no other driving forces.
This article has been cited by other articles:
 |
|
 |
|
  L.-M. Chevin, S. Billiard, and F. Hospital Hitchhiking Both Ways: Effect of Two Interfering Selective Sweeps on Linked Neutral Variation Genetics, September 1, 2008; 180(1): 301 - 316. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. K. Ingvarsson Multilocus Patterns of Nucleotide Polymorphism and the Demographic History of Populus tremula Genetics, September 1, 2008; 180(1): 329 - 340. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. de Meaux, J.-Y. Hu, U. Tartler, and U. Goebel Structurally different alleles of the ath-MIR824 microRNA precursor are maintained at high frequency in Arabidopsis thaliana PNAS, July 1, 2008; 105(26): 8994 - 8999. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Llopart and J. M. Comeron Recurrent Events of Positive Selection in Independent Drosophila Lineages at the Spermatogenesis Gene roughex Genetics, June 1, 2008; 179(2): 1009 - 1020. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Lu, Y. Fu, S. Kumar, Y. Shen, K. Zeng, A. Xu, R. Carthew, and C.-I Wu Adaptive Evolution of Newly Emerged Micro-RNA Genes in Drosophila Mol. Biol. Evol., May 1, 2008; 25(5): 929 - 938. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. J. Cai PGEToolbox: A Matlab Toolbox for Population Genetics and Evolution J. Hered., February 29, 2008; (2008) esm127v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. De Mita, J. Ronfort, H. I. McKhann, C. Poncet, R. El Malki, and T. Bataillon Investigation of the Demographic and Selective Forces Shaping the Nucleotide Diversity of Genes Involved in Nod Factor Signaling in Medicago truncatula Genetics, December 1, 2007; 177(4): 2123 - 2133. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. L. Evans, P. A. Mena, and B. F. McAllister Positive Selection Near an Inversion Breakpoint on the Neo-X Chromosome of Drosophila americana Genetics, November 1, 2007; 177(3): 1303 - 1319. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Wang and J. Zhang Rapid evolution of primate ESX1, an X-linked placenta- and testis-expressed homeobox gene Hum. Mol. Genet., September 1, 2007; 16(17): 2053 - 2060. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Zeng, S. Shi, and C.-I Wu Compound Tests for the Detection of Hitchhiking Under Positive Selection Mol. Biol. Evol., August 1, 2007; 24(8): 1898 - 1908. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Zeng, S. Mano, S. Shi, and C.-I Wu Comparisons of Site- and Haplotype-Frequency Methods for Detecting Positive Selection Mol. Biol. Evol., July 1, 2007; 24(7): 1562 - 1574. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. A. Shapiro, W. Huang, C. Zhang, M. J. Hubisz, J. Lu, D. A. Turissini, S. Fang, H.-Y. Wang, R. R. Hudson, R. Nielsen, et al. Adaptive genic evolution in the Drosophila genomes PNAS, February 13, 2007; 104(7): 2271 - 2276. [Abstract] [Full Text] [PDF]
|
|