Statistical Tests of Neutrality of Mutations Against Population Growth, Hitchhiking and Background Selection

INVESTIGATIONS

Statistical Tests of Neutrality of Mutations Against Population Growth, Hitchhiking and Background Selection

Y. X. Fu
Human Genetics Center, University of Texas, Houston, Texas 77225

The main purpose of this article is to present several new statistical tests of neutrality of mutations against a class of alternative models, under which DNA polymorphisms tend to exhibit excesses of rare alleles or young mutations. Another purpose is to study the powers of existing and newly developed tests and to examine the detailed pattern of polymorphisms under population growth, genetic hitchhiking and background selection. It is found that the polymorphic patterns in a DNA sample under logistic population growth and genetic hitchhiking are very similar and that one of the newly developed tests, F(s), is considerably more powerful than existing tests for rejecting the hypothesis of neutrality of mutations. Background selection gives rise to quite different polymorphic patterns than does logistic population growth or genetic hitchhiking, although all of them show excesses of rare alleles or young mutations. We show that Fu and Li's tests are among the most powerful tests against background selection. Implications of these results are discussed.

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				T. Malausa, L. Leniaud, J.-F. Martin, P. Audiot, D. Bourguet, S. Ponsard, S.-F. Lee, R. G. Harrison, and E. Dopman Molecular Differentiation at Nuclear Loci in French Host Races of the European Corn Borer (Ostrinia nubilalis) Genetics, August 1, 2007; 176(4): 2343 - 2355. [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]

				D. A. Moeller, M. I. Tenaillon, and P. Tiffin Population Structure and Its Effects on Patterns of Nucleotide Polymorphism in Teosinte (Zea mays ssp. parviglumis) Genetics, July 1, 2007; 176(3): 1799 - 1809. [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]

				M. Venkatesan, C. J. Westbrook, M. C. Hauer, and J. L. Rasgon Evidence for a Population Expansion in the West Nile Virus Vector Culex tarsalis Mol. Biol. Evol., May 1, 2007; 24(5): 1208 - 1218. [Abstract] [Full Text] [PDF]

				A. Sanchez-Gracia and J. Rozas Unusual Pattern of Nucleotide Sequence Variation at the OS-E and OS-F Genomic Regions of Drosophila simulans Genetics, April 1, 2007; 175(4): 1923 - 1935. [Abstract] [Full Text] [PDF]

				L. E. Rose, R. W. Michelmore, and C. H. Langley Natural Variation in the Pto Disease Resistance Gene Within Species of Wild Tomato (Lycopersicon). II. Population Genetics of Pto Genetics, March 1, 2007; 175(3): 1307 - 1319. [Abstract] [Full Text] [PDF]

				J. R. S. Meadows, I. Cemal, O. Karaca, E. Gootwine, and J. W. Kijas Five Ovine Mitochondrial Lineages Identified From Sheep Breeds of the Near East Genetics, March 1, 2007; 175(3): 1371 - 1379. [Abstract] [Full Text] [PDF]