Time dependency of molecular rate estimates and systematic overestimation of recent divergence times

Molecular Biology and Evolution

Volumn 22, Issue 7, 2005, Pages 1561-1568

  Ho, Simon Y W ^a   Phillips, Matthew J ^a   Cooper, Alan ^a,b   Drummond, Alexei J ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF ADELAIDE   (Australia)

Author keywords

Mutation rate; Purifying selection; Rate calibration; Substitution rate

Indexed keywords

AVIAN PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BAYES THEOREM; CALIBRATION; CONTROLLED STUDY; EXPERIMENTAL MODEL; GEOLOGICAL TIME; HUMAN; MITOCHONDRION; MOLECULAR CLOCK; MOLECULAR EVOLUTION; MUTATION RATE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIMATE;

ANIMALS; BAYES THEOREM; BIRDS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENETICS, POPULATION; HOMINIDAE; HUMANS; MUTATION; PHYLOGENY; PRIMATES; SPECIES SPECIFICITY; TIME FACTORS; VARIATION (GENETICS);

AVES; PRIMATES;

EID: 20444427160     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi145     Document Type: Article

References (50)

1. Aris-Brosou, S., and Z. Yang. 2002. Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny. Syst. Biol. 51:703-714.
2. Brown, W. M., M. George Jr, and A. C. Wilson. 1979. Rapid evolution of animal mitochondrial DNA. Proc. Natl. Acad. Sci. USA 76:1967-1971.
3. Clark, A. G., and T. S. Whittam. 1992. Sequencing errors and molecular evolutionary analysis. Mol. Biol. Evol. 9:744-752.
4. Drummond, A. J., G. K. Nicholls, A. G. Rodrigo, and W. Solomon. 2002. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161:1307-1320.
5. Drummond, A. J., and A. Rambaut. 2003. BEAST. Version 1.3. Oxford University Press, Oxford, http://evolve.zoc.ox.ac.uk/beast/
6. Fay, J. C., G. J. Wyckoff, and C. I. Wu. 2001. Positive and negative selection on the human genome. Genetics 158:1227-1234.
7. Fleischer, R. C., C. E. McIntosh, and C. L. Tarr. 1998. Evolution on a volcanic conveyor belt: using phylogeographic reconstructions and K-Ar-based ages of the Hawaiian Islands to estimate molecular evolutionary rates. Mol. Ecol. 7:533-545.
8. García-Moreno, J. 2004. Is there a universal mtDNA clock for birds? J. Avian Biol. 35:465-468.
9. Glazko, G. V., and M. Nei. 2003. Estimation of divergence times for major lineages of primate species. Mol. Biol. Evol. 20: 424-434.
10. Hartwig, W. C. 2002. The primate fossil record. Cambridge University Press, Cambridge.
11. Hasegawa, M., Y. Cao, and Z. Yang. 1998. Preponderance of slightly deleterious polymorphism in mitochondrial DNA: nonsynonymous/synonymous rate ratio is much higher within species than between species. Mol. Biol. Evol. 15: 1499-1505.
12. 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.
13. Hedges, S. B., and S. Kumar. 2004. Precision of molecular time estimates. Trends Genet. 202:242-247.
14. Ho, S. Y. W., and L. S. Jermiin. 2004. Tracing the decay of the historical signal in biological sequence data. Syst. Biol. 53:623-637.
15. Holmes, E. C. 2003. Patterns of intra- and interhost nonsynonymous variation reveal strong purifying selection in dengue virus. J. Virol. 77:11296-11298.
16. Horai, S., K. Hayasaka, K. Tsugane, and N. Takhata. 1995. Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs. Proc. Natl. Acad. Sci. USA 92:532-536.
17. Howell, N., I. Kubacka, and D. A. Mackey. 1996. How rapidly does the human mitochondrial genome evolve? Am. J. Hum. Genet. 59:501-509.
18. Howell, N., C. B. Smejkal, D. A. Mackey, P. F. Chinnery, D. M. Turnbull, and C. Herrnstadt. 2003. The pedigree rate of sequence divergence in the human mitochondrial genome: there is a difference between phylogenetic and pedigree rates. Am. J. Hum. Genet. 72:659-670.
19. International Human Genome Sequencing Consortium. 2003. Initial sequencing and analysis of the human genome. Nature 409:860-921.
20. Jazin, E., H. Soodyall, P. Jalonen, E. Lindholm, M. Stoneking, and U. Gyllensten. 1998. Mitochondrial mutation rate revisited: hot spots and polymorphism. Nat. Genet. 18:109-110.
21. Kimura, M. 1983. The neutral theory of molecular evolution. Cambridge University Press, Cambridge.
22. Kolman, C. J., E. Bermingham, R. Cooke, R. H. Ward, T. D. Arias, and F. Guionneau-Sinclair. 1995. Reduced mtDNA diversity in the Ngöbé Amerinds of Panamá. Genetics 140:275-283.
23. Krajewski, C., and D. G. King. 1996. Molecular divergence and phylogeny: rates and patterns of cytochrome b evolution in cranes. Mol. Biol. Evol. 13:21-30.
24. Krings, M., H. Geisert, R. W. Schmitz, H. Krainitzki, and S. Paabo. 1999. DNA sequence of the mitochondrial hypervariable region II from the neandertal type specimen. Proc. Natl. Acad. Sci. USA 96:5581-5585.
25. Krings, M., A. C. 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.
26. Lambert, D. M., P. A. Ritchie, C. D. Millar, B. Holland, A. J. Drummond, and C. Baroni. 2002. Rates of evolution in ancient DNA from Adélie penguins. Science 295: 2270-2273.
27. Martin, R. D. 1986. Primates: a definition. Pp. 1-31 in P. Andrews, ed. Major topics in primate and human evolution. Cambridge University Press, Cambridge.
28. Moilanen, J. S., and K. Majamaa. 2003. Phylogenetic network and physicochemical properties of nonsynonymous mutations in the protein-coding genes of human mitochondrial DNA. Mol. Biol. Evol. 20:1195-1210.
29. Nielsen, R., and D. M. Weinreich. 1999. The age of nonsynonymous and synonymous mutations in animal mtDNA and implications for the mildly deleterious theory. Genetics 153:497-506.
30. Nunn, G. B., and S. E. Stanley. 1998. Body size effects and rates of cytochrome b evolution in tube-nosed seabirds. Mol. Biol. Evol. 15:1360-1371.
31. Ohta, T. 1973. Slightly deleterious mutant substitutions in evolution. Nature 246:96-98.
32. Ohta, T., and M. Kimura. 1971. On the constancy of the evolutionary rate of cistrons. J. Mol. Evol. 1:18-25.
33. Ovchinnikov, I. V., A. Gotherstrom, G. P. Romanova, V. M. Kharitonov, K. Liden, and W. Goodwin. 2000. Molecular analysis of Neanderthal DNA from the northern Caucasus. Nature 404:490-493.
34. Parsons, T. J., D. S. Muniec, K. Sullivan et al. (11 co-authors). 1997. A high observed substitution rate in the human mitochondrial DNA control region. Nat. Genet. 15:363-368.
35. Rambaut, A., and A. J. Drummond. 2004. Tracer. University of Oxford, Oxford.
36. Randi, E. 1996. A mitochondrial cytochrome B phylogeny of the Alectoris partridges. Mol. Phylogenet. Evol. 6:214-227.
37. Raup, D. M., and S. M. Stanley. 1978. Principles of paleontology. W.H. Freeman and Co., San Francisco, Calif.
38. Read, T. D., S. L. Salzberg, M. Pop, M. Shumway, L. Umayam, L. Jiang, E. Holtzapple, J. D. Busch, K. L. Smith, and J. M. Schupp. 2002. Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science 296:2028-2033.
39. Sanderson, M. J. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19:101-109.
40. Schmutz, J., J. Wheeler, J. Grimwood et al. (25 co-authors). 2004. Quality assessment of the human genome sequence. Nature 429:365-368.
41. Schrago, C. G., and C. A. M. Russo. 2003. Timing the origin of New World monkeys. Mol. Biol. Evol. 20:1620-1625.
42. Sigurdardóttir, S., A. Helgason, J. R. Gulcher, K. Stefánsson, and P. Donnelly. 2000. The mutation rate in the human mtDNA control region. Am. J. Hum. Genet. 66:1599-1609.
43. Telfer, P. T., S. Souquiere, S. L. Clifford, K. A. Abernethy, M. W. Bruford, T. R. Disotell, K. N. Sterner, P. Roques, P. A. Marx, and E. J. Wickings. 2003. Molecular evidence for deep phylogenetic divergence in Mandrillus sphinx. Mol. Ecol. 12:2019-2024.
44. Thorne, J. L., H. Kishino, and I. S. Painter. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15:1647-1657.
45. 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.
46. Ward, R. H., B. L. Frazier, K. Dew-Jager, and S. Pääbo. 1991. Extensive mitochondrial diversity within a single Amerindian tribe. Proc. Natl. Acad. Sci. USA 88:8720-8724.
47. Warren, B. H., E. Bermingham, R. C. Bowie, R. P. Prys-Jones, and C. Thebaud. 2003. Molecular phylogeography reveals island colonization history and diversification of western Indian Ocean sunbirds (Nectarinia: Nectariniidae). Mol. Phylogenet. Evol. 29:67-85.
48. Yang, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39:306-314.
49. -. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555-556.
50. Yang, Z., R. Nielsen, N. Goldman, and A. M. Pedersen. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-439.