Statistical Method for Testing the Neutral Mutation Hypothesis by DNA Polymorphism

INVESTIGATIONS

Statistical Method for Testing the Neutral Mutation Hypothesis by DNA Polymorphism

F. Tajima
Department of Biology, Kyushu University, Fukuoka 812, Japan

The relationship between the two estimates of genetic variation at the DNA level, namely the number of segregating sites and the average number of nucleotide differences estimated from pairwise comparison, is investigated. It is found that the correlation between these two estimates is large when the sample size is small, and decreases slowly as the sample size increases. Using the relationship obtained, a statistical method for testing the neutral mutation hypothesis is developed. This method needs only the data of DNA polymorphism, namely the genetic variation within population at the DNA level. A simple method of computer simulation, that was used in order to obtain the distribution of a new statistic developed, is also presented. Applying this statistical method to the five regions of DNA sequences in Drosophila melanogaster, it is found that large insertion/deletion (>100 bp) is deleterious. It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.

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				A. L. Hughes, R. Friedman, P. Rivailler, and J. O. French Synonymous and Nonsynonymous Polymorphisms versus Divergences in Bacterial Genomes Mol. Biol. Evol., October 1, 2008; 25(10): 2199 - 2209. [Abstract] [Full Text] [PDF]

				D. E. Janes, T. Ezaz, J. A. Marshall Graves, and S. V. Edwards Recombination and Nucleotide Diversity in the Sex Chromosomal Pseudoautosomal Region of the Emu, Dromaius novaehollandiae J. Hered., September 4, 2008; (2008) esn065v1. [Abstract] [Full Text] [PDF]

				N. A. Kocabas, P. Aksoy, L. L. Pelleymounter, I. Moon, J.-S. Ryu, J. A. Gilbert, O. E. Salavaggione, B. W. Eckloff, E. D. Wieben, V. Yee, et al. Gemcitabine Pharmacogenomics: Deoxycytidine Kinase and Cytidylate Kinase Gene Resequencing and Functional Genomics Drug Metab. Dispos., September 1, 2008; 36(9): 1951 - 1959. [Abstract] [Full Text] [PDF]

				C. Fan, Y. Zhang, Y. Yu, S. Rounsley, M. Long, and R. A. Wing The Subtelomere of Oryza sativa Chromosome 3 Short Arm as a Hot Bed of New Gene Origination in Rice Mol Plant, September 1, 2008; 1(5): 839 - 850. [Abstract] [Full Text] [PDF]

				J. F. Storz and J. K. Kelly Effects of Spatially Varying Selection on Nucleotide Diversity and Linkage Disequilibrium: Insights From Deer Mouse Globin Genes Genetics, September 1, 2008; 180(1): 367 - 379. [Abstract] [Full Text] [PDF]

				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]

				S. M. Carr and H. D. Marshall Intraspecific Phylogeographic Genomics From Multiple Complete mtDNA Genomes in Atlantic Cod (Gadus morhua): Origins of the "Codmother," Transatlantic Vicariance and Midglacial Population Expansion Genetics, September 1, 2008; 180(1): 381 - 389. [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]

				D. Zivkovic and T. Wiehe Second-Order Moments of Segregating Sites Under Variable Population Size Genetics, September 1, 2008; 180(1): 341 - 357. [Abstract] [Full Text] [PDF]

				Y. Koide, M. Ikenaga, N. Sawamura, D. Nishimoto, K. Matsubara, K. Onishi, A. Kanazawa, and Y. Sano The Evolution of Sex-Independent Transmission Ratio Distortion Involving Multiple Allelic Interactions at a Single Locus in Rice Genetics, September 1, 2008; 180(1): 409 - 420. [Abstract] [Full Text] [PDF]

				P. R. Haddrill, D. Bachtrog, and P. Andolfatto Positive and Negative Selection on Noncoding DNA in Drosophila simulans Mol. Biol. Evol., September 1, 2008; 25(9): 1825 - 1834. [Abstract] [Full Text] [PDF]