Properties of Statistical Tests of Neutrality for DNA Polymorphism Data

INVESTIGATIONS

Properties of Statistical Tests of Neutrality for DNA Polymorphism Data

K. L. Simonsen, G. A. Churchill and C. F. Aquadro
Center for Applied Math, Cornell University, Ithaca, New York 14853

A class of statistical tests based on molecular polymorphism data is studied to determine size and power properties. The class includes TAJIMA's D statistic as well as the D* and F* tests proposed by FU and LI. A new method of constructing critical values for these tests is described. Simulations indicate that TAJIMA's test is generally most powerful against the alternative hypotheses of selective sweep, population bottleneck, and population subdivision, among tests within this class. However, even TAJIMA's test can detect a selective sweep or bottleneck only if it has occurred within a specific interval of time in the recent past or population subdivision only when it has persisted for a very long time. For greatest power against the particular alternatives studied here, it is better to sequence more alleles than more sites.

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				I. Hellmann, K. Prufer, H. Ji, M. C. Zody, S. Paabo, and S. E. Ptak Why do human diversity levels vary at a megabase scale? Genome Res., September 1, 2005; 15(9): 1222 - 1231. [Abstract] [Full Text] [PDF]

				K. K. Nightingale, K. Windham, and M. Wiedmann Evolution and Molecular Phylogeny of Listeria monocytogenes Isolated from Human and Animal Listeriosis Cases and Foods J. Bacteriol., August 15, 2005; 187(16): 5537 - 5551. [Abstract] [Full Text] [PDF]

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