Molecular dating of phylogenies by likelihood methods: A comparison of models and a new information criterion

Molecular Phylogenetics and Evolution

Volumn 67, Issue 2, 2013, Pages 436-444

  Paradis, Emmanuel ^a  

^a CNRS   (France)

Author keywords

Large scale estimation; Molecular dating; Penalised likelihood; Rate smoothing; Relaxed molecular clock

Indexed keywords

ALGORITHM; ANIMAL; ARTICLE; COMPUTER SIMULATION; GENETIC VARIABILITY; MOLECULAR EVOLUTION; PHYLOGENY; THEORETICAL MODEL;

ALGORITHMS; ANIMALS; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; GENETIC VARIATION; MODELS, THEORETICAL; PHYLOGENY;

EID: 84877929456     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2013.02.008     Document Type: Article

References (36)

1. Akaike H. Information theory and an extension of the maximum likelihood principle. Proceedings of the Second International Symposium on Information Theory 1973, 267-281. Akadémia Kiado, Budapest. B.N. Petrov, F. Csaki (Eds.).
2. Britton T., Oxelman B., Vinnersten A., Bremer K. Phylogenetic dating with confidence intervals using mean path lengths. Mol. Phyl. Evol. 2002, 24(1):58-65.
3. Brown R.P., Yang Z. Rate variation and estimation of divergence times using strict and relaxed clocks. BMC Evol. Biol. 2011, 11:271.
4. dos Reis M., Yang Z.H. Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times. Mol. Biol. Evol. 2011, 28(7):2161-2172.
5. Drummond A.J., Ho S.Y.W., Phillips M.J., Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006, 4(5):699-710.
6. Drummond A.J., Rambaut A. BEAST: bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
7. Garland T. Rate tests for phenotypic evolution using phylogenetically independent contrasts. Am. Nat. 1992, 140(3):509-519.
8. Gay, D.M., 1990. Usage summary for selected optimization routines. Tech. Rep. Computing Science Technical Report No. 153, AT& T Bell Laboratories, Murray Hill, NJ 07974, USA. http://netlib.bell-labs.com/netlib/port/.
9. Guindon S. Bayesian estimation of divergence times from large sequence alignments. Mol. Biol. Evol. 2010, 27(8):1768-1781.
10. Ho S.Y.W., Lanfear R. Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks. Mitochondrial DNA 2010, 21(3-4):138-146.
11. Kim J., Sanderson M.J. Penalized likelihood phylogenetic inference: bridging the parsimony-likelihood gap. Syst. Biol. 2008, 57(5):665-674.
12. Konishi S., Kitagawa G. Information Criteria and Statistical Modeling 2008, Springer, New York.
13. Lartillot N., Lepage T., Blanquart S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 2009, 25(17):2286-2288.
14. Lartillot N., Poujol R. A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters. Mol. Biol. Evol. 2011, 28(1):729-744.
15. Lepage T., Bryant D., Philippe H., Lartillot N. A general comparison of relaxed molecular clock models. Mol. Biol. Evol. 2007, 24(12):2669-2680.
16. Magallón S. Fossils to break long branches in molecular dating: a comparison of relaxed clocks applied to the origin of angiosperms. Syst. Biol. 2010, 59(4):384-399.
17. Mayrose I., Otto S.P. A likelihood method for detecting trait-dependent shifts in the rate of molecular evolution. Mol. Biol. Evol. 2011, 28(1):759-770.
18. Nee S., Mooers A.Ø., Harvey P.H. Tempo and mode of evolution revealed from molecular phylogenies. Proc. Natl. Acad. Sci. USA 1992, 89:8322-8326.
19. Paradis E. Analysis of Phylogenetics and Evolution with R 2012, Springer, New York. second ed.
20. Paradis E., Claude J., Strimmer K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 2004, 20(2):289-290.
21. Pereira S.L., Baker A.J. A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock. Mol. Biol. Evol. 2006, 23(9):1731-1740.
22. R Development Core Team, 2012. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria, iSBN 3-900051-07-0. http://www.R-project.org.
23. Sanderson M.J. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 1997, 14(12):1218-1231.
24. Sanderson M.J. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 2002, 19(1):101-109.
25. Sanderson M.J. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 2003, 19(2):301-302.
26. Schnabel R.B., Koontz J.E., Weiss B.E. A modular system of algorithms for unconstrained minimization. ACM Trans. Math. Software 1985, 11(4):419-440.
27. Thorne J.L., Kishino H. Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 2002, 51(5):689-702.
28. Thorne J.L., Kishino H., Painter I.S. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 1998, 15(12):1647-1657.
29. Warren B.H., Bermingham E., Bowie R.C.K., Prys-Jones R.P., Thébaud C. Molecular phylogeography reveals island colonization history and diversification of western Indian Ocean sunbirds (Nectarinia: Nectariniidea). Mol. Phyl. Evol. 2003, 29(1):67-85.
30. Wertheim J.O., Sanderson M.J., Worobey M., Bjork A. Relaxed molecular clocks, the bias-variance trade-off, and the quality of phylogenetic inference. Syst. Biol. 2010, 59(1):1-8.
31. Wilkinson R.D., Steiper M.E., Soligo C., Martin R.D., Yang Z.H., Tavaré S. Dating primate divergences through an integrated analysis of palaeontological and molecular data. Syst. Biol. 2011, 60(1):16-31.
32. Xia X., Yang Q. A distance-based least-square method for dating speciation events. Mol. Phyl. Evol. 2011, 59(2):342-353.
33. Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 1994, 39(3):306-314.
34. Yang Z. A heuristic rate smoothing procedure for maximum likelihood estimation of species divergence times. Acta Zoologica Sinica 2004, 50(4):645-656.
35. Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 2007, 24(8):1586-1591.
36. Yang Z., Rannala B. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol. Biol. Evol. 2006, 23(1):212-226.