How can we distinguish between mutational 'hot spots' and 'old sites' in human mtDNA samples?

Human Biology

Volumn 72, Issue 3, 2000, Pages 455-471

  Gurven, Michael ^a  

^a UNIVERSITY OF NEW MEXICO   (United States)

Author keywords

Ancient demography; Human mtDNA; Mutation rate variation; Population genetics

Indexed keywords

EID: 0034126726     PISSN: 00187143     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (30)

1. Anderson, S., A.T. Bankier, B.G. Barrell et al. 1981. Sequence and organization of the human mitochondrial genome. Nature 290:457-465.
2. Di Rienzo, A., and A.C. Wilson. 1991. Branching pattern in the evolutionary tree for human mitochondrial DNA. Proc. Natl. Acad. Sci. USA 88:1597-1601.
3. Gurven, M.D. 1996. What can we infer from the mtDNA evidence about human demographic history? B.A. thesis. Department of Anthropology. The Pennsylvania State University.
4. Harpending, H.C., S.T. Sherry, A.R. Rogers et al. 1993. The genetic structure of ancient human populations. Curr. Anthropol. 34:483-496.
5. Harpending, H.C., J. Relethford, and S.T. Sherry. 1996. Methods and models for understanding human diversity. In Molecular Biology and Human Diversity, A. Boyce and N. Mascie-Taylor, eds. Cambridge, England: Cambridge University Press, 283-299.
6. Harpending, H.C., M. A. Batzer, M.D. Gurven et al. 1998. Genetic traces of ancient demography. PNAS 95:1961-1967.
7. Hartl, D.L., and A.G. Clark. 1989. Principles of Population Genetics. Cambridge, MA: Sinauer Associates.
8. Hasegawa, M., A. Di Rienzo, T.D. Kocher et al. 1993. Toward a more accurate time scale for the human mitochondrial DNA tree. J. Mol. Evol. 37:347-354.
9. Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mtDNA. J. Mol. Evol. 22:160-174.
10. Horai, S., and K. Hayasaka. 1990. Intra specific nucleotide sequence differences in the major noncoding region of human mitochondrial DNA. Am. J. Hum. Genet. 46:828-842.
11. Howell, N., I. Kubacka, and D.A. Mackey. 1996. How rapidly does the human genome evolve? Am. J. Hum. Genet. 59:501-515.
12. Jukes, T.H., and C.R. Cantor. 1969. Evolution of protein molecules. In Mammalian Protein Metabolism III. H.N. Munro, ed. New York: Academic Press, 21-132.
13. Kimura, M. 1971. Theoretical foundation of population genetics at the molecular level. Theor. Popul. Biol. 2:174-208.
14. Lewontin, R.C. 1964. The interaction of selection and linkage 1. General considerations: heterotic models. Genetics 49:49-67.
15. Lewontin, R.C. 1988. On measures of gametic disequilibrium. Genetics 120:849-852.
16. Lewontin, R.C. 1995. The detection of linkage disequilibrium in molecular sequence data. Genetics 149:377-388.
17. Loewe, L., and S. Scherer. 1997. Mitochondrial Eve: The plot thickens. TREE 12:422-423.
18. Merriwether, D.A., A.G. Clark. S.W. Ballinger et al. 1991. The structure of human mitochondrial DNA variation. J. Mol. Evol. 33:543-555.
19. Pääbo, S. 1996. Mutational hot spots in the mitochondrial microcosm. Am. J. Hum. Genet. 59:493-496.
20. Parsons, T.J., D.S. Muniec, K. Sullivan et al. 1997. A high observed substitution rate in the human mitochondrial DNA control region. Nat. Genet. 15:363-368.
21. Rogers, A.R., and H.C. Harpending. 1992. Population growth makes waves in the distribution of pairwise differences. Mol. Biol. Evol. 9:552-569
22. Rogers, A.R., A.E. Fraley, M.J. Bamshad et al. 1996. Mitochondrial mismatch analysis is insensitive to the mutational process. Mol. Biol. Evol. 13:895-902.
23. Sherry, S.T., A.R. Rogers, H.C. Harpending et al. 1994. Mismatch distributions of mtDNA reveal recent human population expansions. Hum. Biol. 6:761-775.
24. Slatkin, M. 1994. Linkage disequilibrium in growing and stable populations. Genetics 137:331-336.
25. Vigilant, L. 1990. Control region sequences from African populations and the evolution of human mitochondrial DNA. Ph.D. diss. Berkeley, CA: University of California.
26. Wakeley, J. 1993. Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA. J. Mol. Evol. 37:613-623.
27. Wakeley, J. 1994. Substitution rate variation among sites and the estimation of transition bias. Mol. Biol. Evol. 11:436-442.
28. Wakeley, J. 1996. The excess of transitions among nucleotide substitutions: New methods of estimating transition bias underscore its significance. TREE 11:158-163.
29. Yang, Z. 1996. Among-site rate variation and its impact on phylogenetic analyses. TREE 11:367-372.
30. Yang, Z., and S. Kumar. 1996. Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites. Mol. Biol. Evol. 13:650-659.