For example wakeley submitted obtained a 047 for the

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Unformatted text preview: as that for the entire control region, because the former does not include a large segment of apparently invariable sites. For example, Wakeley (submitted) obtained a = 0.47 for the 250-bp 5’ -side hypervariable segment. This value is higher than the value for the entire control region, because the invariable segment is not included. The estimate of a is subject to sampling errors, and theoretically these errors are expected to affect the estimate of d. In practice, however, the effect of these errors is confounded with that of the sampling errors of PI, pz, and d, so that it is difficult to evaluate the effect. In the present case, our estimate of the age of the common ancestral mtDNA in humans was virtually the same as that obtained by Nei ( 1992) without using information on a. Furthermore, the $/a ratio, which is a function of a, was nearly the same for the human-chimpanzee comparison and for the human sequence comparison. These observations suggest that our estimation of a is reliable. Computer Program A computer request. Acknowledgments We would like to thank Mark Stoneking for providing DNA sequence data and John Wakeley for sending an unpublished manuscript. This work was supported by research grants, from the National Institute of Health and the National Science Foundation, to M.N. LITERATURE ANDERSON, DROUIN, SMITH, program for computing d, S: 2, and their variances is available on CITED S., A. T. BANKIER, B. G. BARRELL, M. H. L. DE BRUIJN, A. R. COULSON, J. I. C. EPERON, D. P. NIERLICH, B. A. ROE, F. SANGER, P. H. SCHREIER, A. J. H. R. STADEN, mitochondrial and I. G. YOUNG. 198 1. Sequence genome. Nature 290:457-465. and organization of the human Nucleotide Substitution in mtDNA 525 AQUADRO, C. F., and B. D. GREENBERG. 1983. Human mitochondrial DNA variation and evolution: analysis of nucleotide sequences from seven individuals. Genetics 103:287-3 12. BROWN, W. M., E. M. PRAGER, A. WANG, and A. C. WILSON. 1982. Mitochondrial DNA sequences of primates: tempo and mode of evolution. J. Mol. Evol. l&225-239. CAVALLI-SFORZA, L., A. PIAZZA, P. MENOZZI, and J. MOUNTAIN. 1988. Reconstruction of L. human evolution: bringing together genetic, archaeological, and linguistic data. Proc. Natl. Acad. Sci. USA 85:6002-6006. FERRIS, S. D., W. M. BROWN, W. S. DAVIDSON,and A. C. WILSON. 198 1. Extensive polymorphism in the mitochondrial DNA of apes. Proc. Natl. Acad. Sci. USA 78:6319-6323. FITCH, W. M., and E. MARGOLIASH. 1967. A method for estimating the number of invariant amino acid coding positions in a gene using cytochrome c as a model case. Biochem. Genet. 1:65-7 1. GOJOBORI,T., W.-H. LI, and D. GRAUR. 1982. Patterns of nucleotide substitution in pseudogenes and functional genes. J. Mol. Evol. l&360-369. HASEGAWA,M., and S. HORAI. 199 1. Time of the deepest root for polymorphism in human mitochondrial DNA. J. Mol. Evol. 32:37-42. HASEGAWA,M., H. KISHINO, and T. YANO. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22: 160-174. HEDGES,S. B., S. KUMAR, K. TAMURA,and M. STONEKING. 1992. Human origins and analysis of mitochondrial DNA sequences. Science 255:737-739. HORAI, S., and K. HAYASAKA . 1990. Intraspecific nucleotide sequence differences in the major noncoding region of human mitochondrial DNA. Am. J. Hum. Genet. 46:828-842. JIN, L., and M. NEI . 1990. Limitation of the evolutionary parsimony method of phylogenetic analysis. Mol. Biol. Evol. 7:82-102. JOHNSON,N. L., and S. KOTZ. 1973. Distributions in statistics: discrete distributions. HoughtonMifflin, Boston. KIMURA, M. 1980. A simple method for estimating evolutionary rate o...
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