Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation

Molecular Biology and Evolution

Volumn 22, Issue 5, 2005, Pages 1355-1363

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

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Bayesian inference; Cambrian explosion; Molecular rates; Penalized likelihood; Relaxed clock

Indexed keywords

ARTICLE; ARTIFACT; BAYES THEOREM; CAMBRIAN; EVOLUTIONARY RATE; GENETIC VARIABILITY; METAZOON; MOLECULAR CLOCK; NONHUMAN; NUCLEOTIDE SEQUENCE; SIMULATION;

ALGORITHMS; ANIMALS; BAYES THEOREM; EVOLUTION, MOLECULAR; INVERTEBRATES; LIKELIHOOD FUNCTIONS; MARKOV CHAINS; MODELS, GENETIC; PHYLOGENY; TIME FACTORS;

EID: 17744387938     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi125     Document Type: Article

References (32)

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. _. 2003. Bayesian models of episodic evolution support a Precambrian explosive diversification of the Metazoa. Mol. Biol. Evol. 20:1947-1954.
3. Bromham, L., D. Penny, A. Rambaut, and M. D. Hendy. 2000. The power of relative rates tests depends on the data. J. Mol. Evol. 50:296-301.
4. Bromham, L., A. Rambaut, R. Fortey, A. Cooper, and D. Penny. 1998. Testing the Cambrian explosion hypothesis by using a molecular dating technique. Proc. Natl. Acad. Sci. USA 95:12386-12389.
5. Bromham, L. D., and M. D. Hendy. 2000. Can fast early rates reconcile molecular dates with the Cambrian explosion? Proc. R. Soc. Lond. B Biol. Sci. 267:1041-1047.
6. Cooper, A., and D. Penny. 1997. Mass survival of birds across the Cretaceous-Tertiary boundary: molecular evidence. Science 275:1109-1113.
7. Cutler, D. J. 2000. Estimating divergence times in the presence of an overdispersed molecular clock. Mol. Biol. Evol. 17:1647-1660.
8. 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.
9. Foster, P. G. 2004. Modelling compositional heterogeneity. Syst. Biol. 53:485-495.
10. 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.
11. Huelsenbeck, J. P., B. Larget, and D. L. Swofford. 2000. A compound Poisson process for relaxing the molecular clock. Genetics 154:1879-1892.
12. Huelsenbeck, J. P., and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
13. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules. Pp. 21-132 in H. N. Munro, ed. Mammalian protein metabolism. Academic Press, New York.
14. Kass, R. E., and A. E. Raftery. 1995. Bayes factors. J. Am. Stat. Assoc. 90:773-795.
15. Kishino, H., J. L. Thorne, and W. J. Bruno. 2001. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18:352-361.
16. Perez-Losada, M., J. T. Hoeg, and K. A. Crandall. 2004. Unraveling the evolutionary radiation of the thoracican barnacles using molecular and morphological evidence: a comparison of several divergence time estimation approaches. Syst. Biol. 53:244-264.
17. Rambaut, A. 2000. Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics 16:395-399.
18. Rambaut, A., and L. Bromham. 1998. Estimating divergence dates from molecular sequences. Mol. Biol. Evol. 15:442-448.
19. Rambaut, A., and A. J. Drummond. 2004. Tracer. University of Oxford, Oxford.
20. Rambaut, A., and N. C. Grassly. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238.
21. Sanderson, M. J. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14:1218-1231.
22. _. 1998. Estimating rate and time in molecular phylogenies: beyond the molecular clock? Pp. 242-264 in D. E. Soltis, P. S. Soltis, and J. J. Doyle, eds. Molecular systematics of plants II: DNA sequencing. Kluwer Academic Publishers, Norwell, Mass.
23. _. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19:101-109.
24. _. 2003. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19:301-302.
25. Spiegelhalter, D. J., N. G. Best, B. P. Carlin, and A. van der Linde. 2002. Bayesian measures of model complexity and fit (with discussion). J. R. Stat. Soc. Ser. B 64:583-639.
26. Takezaki, N., A. Rzhetsky, and M. Nei. 1995. Phylogenetic test of the molecular clock and linearized trees. Mol. Biol. Evol. 12:823-833.
27. Thorne, J. L., and H. Kishino. 2002. Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51:689-702.
28. 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.
29. Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.
30. Yang, Z., and B. Rannala. 1997. Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo Method. Mol. Biol. Evol. 14:717-724.
31. Yang, Z., and A. D. Yoder. 2003. Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute-looking mouse lemur species. Syst. Biol. 52:705-716.
32. Yoder, A. D., and Z. H. Yang. 2000. Estimation of primate speciation dates using local molecular clocks. Mol. Biol. Evol. 17:1081-1090.