Received date: 2019-01-14
Online published: 2019-07-20
This paper provides an overview and a protocol of molecular clock dating using MrBayes. Two modern approaches, total-evidence dating and node dating, are demonstrated using a truncated dataset of Hymenoptera with molecular sequences and morphological characters. The similarity and difference of the two methods are compared and discussed. Besides, a non-clock analysis is performed on the same dataset to compare with the molecular clock dating analyses.
Key words: Bayesian phylogenetic inference; molecular clock dating; MCMC; MrBayes
ZHANG Chi . Molecular clock dating using MrBayes[J]. Vertebrata Palasiatica, 2019 , 57(3) : 241 -252 . DOI: 10.19615/j.cnki.1000-3118.190408
[1] | Altekar G, Dwarkadas S, Huelsenbeck J P et al., 2004. Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics, 20:407-415 |
[2] | Ayres D L, Darling A, Zwickl D J et al., 2012. BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics. Syst Biol, 61:170-173 |
[3] | Drummond A J, Ho S Y W, Phillips M J et al., 2006. Relaxed phylogenetics and dating with confidence. PLoS Biol, 4:e88 |
[4] | Gavryushkina A, Welch D, Stadler T et al., 2014. Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration. PLoS Comput Biol, 10:e1003919 |
[5] | Hastings W K, 1970. Monte Carlo sampling methods using Markov chains and their applications. Biometrika, 57:97-109 |
[6] | Heath T A, Huelsenbeck J P, Stadler T, 2014. The fossilized birth-death process for coherent calibration of divergence-time estimates. Proc Natl Acad Sci USA, 111:e2957-2966 |
[7] | Ho S Y W, Phillips M J, 2009. Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst Biol, 58:367-380 |
[8] | H?hna S, Stadler T, Ronquist F et al., 2011. Inferring speciation and extinction rates under different sampling schemes. Mol Biol Evol, 28:2577-2589 |
[9] | Huelsenbeck J P, Larget B, Swofford D L, 2000. A compound Poisson process for relaxing the molecular clock. Genetics, 154:1879-1892 |
[10] | Lakner C, van der Mark P, Huelsenbeck J P et al., 2008. Efficiency of Markov chain Monte Carlo tree proposals in Bayesian phylogenetics. Syst Biol, 57:86-103 |
[11] | Lepage T, Bryant D, Philippe H et al., 2007. A general comparison of relaxed molecular clock models. Mol Biol Evol, 24:2669-2680 |
[12] | Lewis P O, 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Syst Biol, 50:913-925 |
[13] | Liu L, 2008. BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics, 24:2542-2543 |
[14] | Liu L, Yu L, Kubatko L et al., 2009. Coalescent methods for estimating phylogenetic trees. Mol Phylogenet Evol, 53:320-328 |
[15] | Metropolis N, Rosenbluth A W, Rosenbluth M N et al., 1953. Equation of state calculations by fast computing machines. J Chem Phys, 21:1087-1092 |
[16] | Rannala B, Zhu T, Yang Z, 2012. Tail paradox, partial identifiability, and influential priors in Bayesian branch length inference. Mol Biol Evol, 29:325-335 |
[17] | Ronquist F, Huelsenbeck J P, 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19:1572-1574 |
[18] | Ronquist F, Klopfstein S, Vilhelmsen L et al., 2012a. A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera. Syst Biol, 61:973-999 |
[19] | Ronquist F, Teslenko M, van der Mark P et al., 2012b. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol, 61:539-542 |
[20] | Stadler T, 2010. Sampling-through-time in birth-death trees. J Theoret Biol, 267:396-404 |
[21] | Thorne J L, Kishino H, 2002. Divergence time and evolutionary rate estimation with multilocus data. Syst Biol, 51:689-702 |
[22] | Van Noorden R, Maher B, Nuzzo R, 2014. The top 100 papers. Nature, 514:550-553 |
[23] | Xie W, Lewis P O, Fan Y et al., 2011. Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Syst Biol, 60:150-160 |
[24] | Yang Z, 1994a. Estimating the pattern of nucleotide substitution. J Mol Evol, 39:105-111 |
[25] | Yang Z, 1994b. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol, 39:306-314 |
[26] | 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 |
[27] | Zhang C, Rannala B, Yang Z, 2012. Robustness of compound Dirichlet priors for Bayesian inference of branch lengths. Syst Biol, 61:779-784 |
[28] | Zhang C, Stadler T, Klopfstein S et al., 2016. Total-evidence dating under the fossilized birth-death process. Syst Biol, 65:228-249 |
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