Testing for equality of molecular evolutionary rates: A comparison between a relative-rate test and a likelihood ratio test

Molecular Biology and Evolution

Volumn 16, Issue 6, 1999, Pages 849-855

  Sorhannus, Ulf ^a   Van Bell, Craig ^b  

^a EDINBORO UNIVERSITY OF PENNSYLVANIA   (United States)

^b NONE

Author keywords

Divergence time; Likelihood ratio test; Molecular clock; Nucleotide substitution rate; Phylogeny; Relative rate test; Simulation

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; MATHEMATICAL ANALYSIS; MOLECULAR EVOLUTION; MOLECULAR MODEL; PHYLOGENY; SIMULATION;

EID: 0033015734     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026169     Document Type: Article

References (41)

1. AYALA, F. J., A. RZHETSKY, and F. J. AYALA. 1998. Origin of the metazoan phyla: molecular clocks confirm paleontological estimates. Proc. Natl. Acad. Sci. USA 95:606-611.
2. BOUSQUET, J., S. H. STRAUSS, and P. LI. 1992. Complete congruence between morphological and rbcL-based molecular phylogenies in birches and related species (Betulaceae). Mol. Biol. Evol. 9:1076-1088.
3. BRITTEN, R. J. 1986. Rates of DNA evolution differs between taxonomic groups. Science 231:1393-1398.
4. DAUGBJERG, N., and R. A. ANDERSEN. 1997. A molecular phylogeny of the heterokont algae based on analyses of chloroplast-encoded rbcL sequence data. J. Phycol. 33:1031-1041.
5. DOOLITTLE, R. F., D.-F. FENG, S. TSANG, G. CHO, and E. LITTLE. 1996. Determining divergence times of the major kingdoms of living organisms with a protein clock. Nature 271: 470-477.
6. FELSENSTEIN, J. 1981. Evolutionary trees and DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
7. _. 1988. Phylogenies from molecular sequences: inference and reliability. Annu. Rev. Genet. 22:521-565.
8. _. 1993. PHYLIP (phylogeny inference package). Version 3.5c. Distributed by the author, Department of Genetics, University of Washington, Seattle.
9. GAUT, B. S., S. V. MUSE, W. D. CLARK, and M. T. CLEGG. 1992. Relative rates of nucleotide substitution at the rbcL locus of monocotyledonous plants. J. Mol. Evol. 13:292-303.
10. GILLESPIE, J. H. 1986. Rates of molecular evolution. Annu. Rev. Ecol. Syst. 17:637-665.
11. GOLDMAN, N. 1993. Statistical tests of models of DNA substitution. J. Mol. Evol. 36:182-198.
12. HILLIS, D. M., J. P. HUELSENBECK, and C. W. CUNNINGHAM. 1994. Application and accuracy of molecular phylogenies. Science 264:671-677.
13. KIMURA, M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
14. KOOISTRA, W. H. C. F., and L. K. MEDLIN. 1996. Evolution of the diatoms (Bacillariophyta), IV. A reconstruction of their age from small subunit rRNA coding regions and the fossil record. Mol. Phylogenet. Evol. 6:391-407.
15. KUMAR, S., and S. B. HEDGES. 1998. A molecular timescale for vertebrate evolution. Nature 392:917-920.
16. LI, P., and J. BOUSQUET. 1992. Relative-rate test for nucleotide substitutions between two lineages. Mol. Biol. Evol. 9: 1185-1189.
17. LI, W.-H., and M. TANIMURA. 1987. The molecular clock runs more slowly in man than in apes and monkeys. Nature 328: 93-96.
18. LI, W.-H., C.-I. WU, and C.-C. LUO. 1985. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2:150-174.
19. MARSHALL, C. R. 1990a. The fossil record and estimating divergence times between lineages: maximum divergence times and the importance of reliable phylogenies. J. Mol. Evol. 30:400-408.
20. _. 1990b. Confidence intervals on stratigraphic ranges. Paleobiology 16:1-10.
21. MUSE, S. V., and B. S. WEIR. 1992. Testing for equality of evolutionary rates. Genetics 132:269-276.
22. OLIVER, J. L., A. MARIN, and J.-R. MEDINA. 1989. SDSE: a software package to simulate the evolution of a pair of DNA sequences. CABIOS 5:47-50.
23. PAGE, R. D. M. 1996. TREEVIEW: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12:357-358.
24. PALUMBI, S. R. 1989. Rate of molecular evolution and the fraction of nucleotide positions free to vary. J. Mol. Evol. 29: 180-187.
25. PHILIPPE, H., U. SORHANNUS, A. BAROIN, R. PERASSO, F. GASSE, and A. ADOUTTE. 1994. Comparison of molecular and paleontological data in diatoms suggests a major gap in the fossil record. J. Evol. Biol. 7:247-265.
26. ROBINSON, M., M. GOUY, C. GAUTIER, and D. MOUCHIROUD. 1998. Sensitivity of the relative rate test to taxonomic sampling. Mol. Biol. Evol. 15:1091-1098.
27. RODRIGUEZ, F., J. L. OLIVER, A. MARIN, and J. R. MEDINA. 1990. The general stochastic model of nucleotide substitutions. J. Theor. Biol. 142:485-501.
28. SAITOU, N., and M. NEI. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
29. SARICH, V. M., and A. C. WILSON. 1967. Immunological time scale for hominid evolution. Science 158:1200-1203.
30. _. 1973. Generation time and genomic evolution in primates. Science 179:1144-1147.
31. SCHERER, S. 1989. The relative rate test of molecular clock hypothesis: a note of caution. Mol. Biol. Evol. 6:436-441.
32. _. 1990. The protein molecular clock: time for a reevaluation. Pp. 83-106 in M. K. HECHT, B. WALLACE, and R. J. MACINTYRE, eds. Evolutionary biology. Plenum Press, New York.
33. SMITH A. B., and D. T. J. LITTLEWOOD. 1994. Paleontological data and molecular phylogenetic analysis. Paleobiology 20: 259-273.
34. SORHANNUS, U. 1994. Relative rate tests versus paleontological divergence data for diatoms and vertebrates. Acta Palaeontol. Pol. 38:199-214.
35. STRAUSS, D., and P. M. SADLER. 1989. Classical confidence intervals and Bayesian probability estimates for ends of local taxon ranges. Math. Geol. 21:411-427.
36. TAKEZAKI, N., A. RZHETSKY, and M. NEI. 1995. Phylogenetic test of the molecular clock and linearized trees. Mol. Biol. Evol. 12:823-833.
37. WILSON, A. C., S. S. CARLSON, and T. J. WHITE. 1977. Biochemical evolution. Annu. Rev. Biochem. 46:573-639.
38. WRAY, G. A., J. S. LEVINTON, and L. H. SHAPIRO. 1996. Molecular evidence for deep Precambrian divergences among Metazoan phyla. Science /:568-574.
39. WU, C.-I., and W.-H. LI. 1985. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl. Acad. Sci. USA 82:1741-1745.
40. YANG, Z., N. GOLDMAN, and A. FRIDAY. 1995. Maximum likelihood trees from DNA sequences: a peculiar statistical estimation problem. Syst. Biol. 44:384-399.
41. ZUCKERKANDL, E., and L. PAULING. 1965. Evolutionary divergence and convergence in proteins. Pp. 97-166 in V. BRYSON and H. VOGEL, eds. Evolving genes and proteins. Academic Press, New York.