Geographic origin of human mitochondrial DNA: Accommodating phylogenetic uncertainty and model comparison

Systematic Biology

Volumn 51, Issue 1, 2002, Pages 155-165

  Huelsenbeck, John P ^a   Imennov, Nikita S ^a  

^a UNIVERSITY OF ROCHESTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

AFRICA; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; COMPARATIVE STUDY; GENETICS; HUMAN; MOLECULAR EVOLUTION; PHYLOGENY; STATISTICAL ANALYSIS;

AFRICA; BAYES THEOREM; DATA INTERPRETATION, STATISTICAL; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; HUMANS; MODELS, GENETIC; PHYLOGENY;

EID: 0036005522     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/106351502753475934     Document Type: Article

References (42)

1. Adcock, G. J., E. S. Dennis, S. Easteal, G. A. Huttley, L. S. Jermin, W. J. Peacock, and A. Thorne. 2001. Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins. Proc. Nat. Acad. Sci. USA 98:537-542.
2. Awadalla, P., A. Eyre-Walker, and J. M. Smith. 1999. Linkage disequilibrium and recombination in Hominid mitochondrial DNA. Science 286:2524-2525.
3. Beerli, P., and J. Felsenstein. 1999. Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 152:763-773.
4. Cann, R. L., M. Stoneking, and A. C. Wilson. 1987. Mitochondrial DNA and human evolution. Nature 325:31-36.
5. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17:368-376.
6. Fitch, W. M. 1971. Toward defining the course of evolution: Minimum change for a specific tree topology. Syst. Zool. 20:406-416.
7. Geyer, C. J. 1991. Markov chain Monte Carlo maximum likelihood. Pages 156-163 in Computing science and statistics: Proceedings of the 23rd Symposium on the Interface (E. Keramidas, ed.). Interface Foundation, Fairfax Station, Virginia.
8. Green, P. J. 1995. Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82:711-732.
9. Handt, O., S. Meyer, and A. von Haeseler. 1998. Compilation of human mtDNA control region sequences. Nucleic Acids Res. 26:126-129.
10. Hastings, W. K. 1970. Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57:97-109.
11. Huelsenbeck, J. P., B. Rannala, and J. P. Masly. 2000. Accommodating phylogenetic uncertainty in evolutionary studies. Science 288:2349-2350.
12. Huelsenbeck, J. P., and F. Ronquist. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics. 17:754-755
13. Jeffreys, H. 1935. Some tests of significance, treated by the theory of probability. Proc. Cambridge Philos. Soc. 31:203-222.
14. Jeffreys, H. 1961. Theory of probability. Oxford Univ. Press, Oxford.
15. Krings, M., A. Stone, R. W. Schmitz, H. Krainitzki, M. Stoneking, and S. Pääbo. 1997. Neandertal DNA sequences and the origin of modern humans. Cell 90:19-30.
16. Larget, B., and D. Simon. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16:750-759.
17. Lavine, M., and M. J. Schervish. 1999. Bayes factors: What they are and what they are not. Am. Stat. 53:119-122.
18. Li, S. 1996. Phylogenetic tree construction using Markov chain Monte Carlo. Ph.D. dissertation, Ohio State Univ., Columbus.
19. Maddison, D. R., M. Ruvolo, and D. L. Swofford. 1992. Geographic origins of human mitochondrial DNA: Phylogenetic evidence from control region sequences. Syst. Biol. 41:111-124.
20. Mau, B. 1996. Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Ph.D. Dissertation, Univ. of Wisconsin, Madison.
21. Mau, B., and M. Newton. 1997. Phylogenetic inference for binary data on dendrograms using Markov chain Monte Carlo. J. Comput. Graph. Stat. 6:122-131.
22. Mau, B., M. Newton, and B. Larget. 1999. Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics 55:1-12.
23. Metropolis, N., A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller. 1953. Equations of state calculations by fast computing machines. J. Chem. Phys. 21:1087-1091.
24. Newton, M., B. Mau, and B. Larget. 1999. Markov chain Monte Carlo for the Bayesian analysis of evolutionary trees from aligned molecular sequences. In Statistics in molecular biology (F. Seillier-Moseiwitch, T. P. Speed, and M. Waterman, eds.). Monograph Series of the Institute of Mathematical Statistics.
25. Pagel, M. 1999. The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Syst. Biol. 48:612-622.
26. Penny, D., M. Steel, P. J. Waddell, and M. D. Hendy. 1995. Improved analyses of human mtDNA sequences support a recent African origin for Homo sapiens. Mol. Biol. Evol. 12:863-882.
27. Raftery, A. 1995. Hypothesis testing and model selection. Pages 163-187 in Markov chain Monte Carlo in Practice (W. R. Gilks, S. Richardson, and D. J. Spiegelhalter, eds.). Chapman and Hall, New York.
28. Rannala, B., and Z. Yang. 1996. Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference. J. Mol. Evol. 43:304-311.
29. Schluter, D. 1995. Uncertainty in ancient phylogenies. Nature 377:108-109.
30. Schluter, D., T. Price, A. Ø. Mooers, and D. Ludwig. 1997. Likelihood of ancestor states in adaptive radiation. Evolution 51:1699-1711.
31. Schultz, T. R., and G. A. Churchill. 1999. The role of subjectivity in reconstructing ancestral character states: A Bayesian approach to unknown rates, states, and transformation asymmetries. Syst. Biol. 48:651-664.
32. Stringer, C., and R. McKie. 1996. African exodus. Jonathan Cape, London.
33. Swofford, D. L. 1998. PAUP*: Phylogenetic analysis using parsimony (*and other methods). Sinauer Associates, Sunderland, Massachusetts.
34. Swofford, D., G. Olsen, P. Waddell, and D. M. Hillis. 1996. Phylogenetic inference. Pages 407-511 in Molecular systematics, 2nd edition (D. Hillis, C. Moritz, and B. Mable, eds.). Sinauer Associates, Sunderland, Massachusetts.
35. Tavaré, S. 1986. Some probabilistic and statistical problems on the analysis of DNA sequences. Lect. Math. Life Sci. 17:57-86.
36. Tierney, L. 1994. Markov chains for exploring posterior distributions (with discussion). Ann. Stat. 22:1701-1762.
37. Underhill, P. A., P. Shen, A. A. Lin, L. Jin, G. Passarino, W. H. Yang, E. Kauffman, B. Bonné-Tamir, J. Bertranpetit, P. Francalacci, et al. 2000. Y chromosome sequence variation and the history of human populations. Nat. Genet. 26:358-361.
38. Vigilant, L., M. Stoneking, H. Harpending, K. Hawkes, and A. C. Wilson. 1991. African populations and the evolution of human mitochondrial DNA. Science 253:1503-1507.
39. Wolpoff, M., and R. Caspari. 1997. Race and human evolution. Simon and Schuster, New York.
40. Yang, Z. 1993. Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10:1396-1401.
41. Yang, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J. Mol. Evol. 39:306-314.
42. Yang, Z., and B. Rannala. 1997. Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method. Mol. Biol. Evol. 14:717-724.