Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci

Systematic Biology

Volumn 64, Issue 2, 2015, Pages 267-280

  Zhu, Tianqi ^a   Reis, Mario Dos ^b   Yang, Ziheng ^a,b  

^a Chinese Academy of Sciences   (China)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Bayesian inference; Divergence time; Finite sites theory; Infinite sites theory; Posterior variance; Relaxed clock

Indexed keywords

PRIMATES;

ANIMAL; BIOLOGICAL MODEL; CLASSIFICATION; COMPUTER SIMULATION; DNA SEQUENCE; FOSSIL; GENETICS; PHYLOGENY; PRIMATE; PROCEDURES; TIME; UNCERTAINTY;

ANIMALS; CLASSIFICATION; COMPUTER SIMULATION; FOSSILS; MODELS, GENETIC; PHYLOGENY; PRIMATES; SEQUENCE ANALYSIS, DNA; TIME; UNCERTAINTY;

EID: 84927688256     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syu109     Document Type: Article

References (32)

1. Benton M.J., Donoghue P.C.J. Asher R.J. 2009. Calibrating and constraining molecular clocks. In: Hedges B. S., Kumar S., editors. The Timetree of life. (Oxford, England: Oxford University Press. p. 35-86.
2. Bracken-Grissom H.D., Ahyong S.T., Wilkinson R.D., Feldmann R.M., Schweitzer C.E., Breinholt J.W., Bendall M., Palero F., Chan T.-Y., Felder D.L., Robles R., Chu K.-H., Tsang L.-M., Kim D., Martin J.W., Crandall K.A. 2014. The emergence of lobsters: phylogenetic relationships, morphological evolution and divergence time comparisons of an ancient group (Decapoda: Achelata, Astacidea, Glypheidea, Polychelida). Syst. Biol. 63: 457-479.
3. Britton T. 2005. Estimating divergence times in phylogenetic trees without a molecular clock. Syst. Biol. 54:500-507.
4. Christin P.A., Spriggs E., Osborne C.P., Stromberg C.A., Salamin N., Edwards E.J. 2014. Molecular dating, evolutionary rates, and the age of the grasses. Syst. Biol. 63:153-165.
5. dos Reis M., Inoue J., Hasegawa M., Asher R., Donoghue P.C., Yang Z. 2012. Phylogenomic data sets provide both precision and accuracy in estimating the timescale of placental mammal evolution. Proc. R. Soc. Lond. B. Biol. Sci. 279:3491-3500.
6. dos Reis M., Yang Z. 2013. The unbearable uncertainty of Bayesian divergence time estimation. J. Syst. Evol. 51:30-43.
7. dos Reis M., Zhu T., Yang Z. 2014. The impact of the rate prior on Bayesian estimation of divergence times with multiple loci. Syst. Biol. 63:555-565.
8. Drummond A.J., Ho S.Y.W., Phillips M.J., Rambaut A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4:e88.
9. Drummond A.J., Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214.
10. Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
11. Graur D., Martin W. 2004. Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends Genet. 20:80-86.
12. Hasegawa M., Kishino H., Yano T. 1985. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
13. Heath T.A., Holder M.T., Huelsenbeck J.P. 2012. A Dirichlet process prior for estimating lineage-specific substitution rates. Mol. Biol. Evol. 29:939-955.
14. Ho S.Y.W. Forthcoming 2014. The changing face of the molecular evolutionary clock. Trends. Ecol. Evol.
15. Inoue J., Donoghue P.C.H., Yang Z. 2010. The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Syst. Biol. 59:74-89.
16. Jukes T.H., Cantor C.R. 1969. Evolution of protein molecules. In: Munro H.N., editor. Mammalian protein metabolism. New York: Academic Press. p. 21-123.
17. Kishino H., Thorne J.L., Bruno W.J. 2001. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18:352-361.
18. Lartillot N., Lepage T., Blanquart S. 2009. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25:2286-2288.
19. Lepage T., Bryant D., Philippe H., Lartillot N. 2007. A general comparison of relaxed molecular clock models. Mol. Biol. Evol. 24:2669-2680.
20. Mulcahy D.G., Noonan B.P., Moss T., Townsend T.M., Reeder T.W., Sites J.W., Jr., Wiens J.J. 2012. Estimating divergence dates and evaluating dating methods using phylogenomic and mitochondrial data in squamate reptiles. Mol. Phylogenet. Evol. 65:974-991.
21. Rannala B., Yang Z. 2007. Inferring speciation times under an episodic molecular clock. Syst. Biol. 56:453-466.
22. Ronquist F., Klopfstein S., Vilhelmsen L., Schulmeister S., Murray D.L., Rasnitsyn A.P. 2012a. A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera. Syst. Biol. 61:973-999.
23. Ronquist F., Teslenko M., van der Mark P., Ayres D.L., Darling A., Hohna S., Larget B., Liu L., Suchard M.A., Huelsenbeck J.P. 2012b. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61:539-542.
24. Stamatakis A., Aberer A.J., Goll C., Smith S.A., Berger S.A., Izquierdo-Carrasco F. 2012. RAxML-Light: a tool for computing terabyte phylogenies. Bioinformatics 28:2064-2066.
25. Tavaré S. 1986. Some probabilistic and statistical problems on the analysis of DNA sequences. Lect. Math. Life Sci. 17:57-86.
26. Thorne J.L., Kishino H. 2002. Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51:689-702.
27. Thorne J.L., Kishino H., Painter I.S. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15:1647-1657.
28. Wilkinson R.D., Steiper M.E, Soligo C., Martin R.D., Yang Z., Tavare S. 2011. Dating primate divergences through an integrated analysis of palaeontological and molecular data. Syst. Biol. 60:16-31.
29. Yang Z. 1994a. Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39:105-111.
30. Yang Z. 1994b. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39:306-314.
31. Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24:1586-1591.
32. Yang Z., Rannala B. 2006. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol. Biol. Evol. 23:212-226.