logo

SCIENTIA SINICA Vitae, Volume 49 , Issue 4 : 472-483(2019) https://doi.org/10.1360/N052018-00224

Beyesian molecular dating with genomic data

More info
  • ReceivedJan 30, 2019
  • AcceptedMar 6, 2019
  • PublishedApr 15, 2019

Abstract


Funded by

国家自然科学基金(31671370,31301093,11201224,11301294)

中国科学院青年创新促进会基金(2015080)


Acknowledgment

感谢英国伦敦大学杨子恒教授对文章提出的建设性意见.


References

[1] Xia X, Yang Q. A distance-based least-square method for dating speciation events. Mol Phylogenet Evol, 2011, 59: 342-353 CrossRef PubMed Google Scholar

[2] Tamura K, Battistuzzi F U, Billing-Ross P, et al. Estimating divergence times in large molecular phylogenies. Proc Natl Acad Sci USA, 2012, 109: 19333-19338 CrossRef PubMed ADS Google Scholar

[3] Paradis E. Molecular dating of phylogenies by likelihood methods: A comparison of models and a new information criterion. Mol Phylogenet Evol, 2013, 67: 436-444 CrossRef PubMed Google Scholar

[4] Fourment M, Holmes E C. Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data. BMC Evol Biol, 2014, 14: 163-172 CrossRef PubMed Google Scholar

[5] Ho S Y W, Duchêne S. Molecular-clock methods for estimating evolutionary rates and timescales. Mol Ecol, 2014, 23: 5947-5965 CrossRef PubMed Google Scholar

[6] Thorne J L, Kishino H, Painter I S. Estimating the rate of evolution of the rate of molecular evolution. Mol Biol Evol, 1998, 15: 1647-1657 CrossRef PubMed Google Scholar

[7] Drummond A J, Ho S Y W, Phillips M J, et al. Relaxed phylogenetics and dating with confidence. PLoS Biol, 2006, 4: e88 CrossRef PubMed Google Scholar

[8] 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: 212-226 CrossRef PubMed Google Scholar

[9] Lepage T, Bryant D, Philippe H, et al. A general comparison of relaxed molecular clock models. Mol Biol Evol, 2007, 24: 2669-2680 CrossRef PubMed Google Scholar

[10] Kishino H, Thorne J L, Bruno W J. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol Biol Evol, 2001, 18: 352-361 CrossRef PubMed Google Scholar

[11] Thorne J L, Kishino H. Divergence time and evolutionary rate estimation with multilocus data. Syst Biol, 2002, 51: 689-702 CrossRef PubMed Google Scholar

[12] Drummond D A, Raval A, Wilke C O. A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol, 2006, 23: 327-337 CrossRef PubMed Google Scholar

[13] Rannala B, Yang Z. Inferring speciation times under an episodic molecular clock. Syst Biol, 2007, 56: 453-466 CrossRef PubMed Google Scholar

[14] Stadler T. Sampling-through-time in birth–death trees. J Theor Biol, 2010, 267: 396-404 CrossRef PubMed Google Scholar

[15] Gavryushkina A, Heath T A, Ksepka D T, et al. Bayesian total-evidence dating reveals the recent crown radiation of penguins. Syst Biol, 2016, 64: syw060 CrossRef PubMed Google Scholar

[16] dos Reis M, Donoghue P C J, Yang Z. Bayesian molecular clock dating of species divergences in the genomics era. Nat Rev Genet, 2016, 17: 71-80 CrossRef PubMed Google Scholar

[17] Donoghue P C J, Yang Z. The evolution of methods for establishing evolutionary timescales. Phil Trans R Soc B, 2016, 371: 20160020 CrossRef PubMed Google Scholar

[18] Britton T. Estimating divergence times in phylogenetic trees without a molecular clock. Syst Biol, 2005, 54: 500-507 CrossRef PubMed Google Scholar

[19] Dos Reis M, Yang Z. The unbearable uncertainty of bayesian divergence time estimation. J Syst Evol, 2013, 51: 30-43 CrossRef Google Scholar

[20] Inoue J, Donoghue P C J, Yang Z. The impact of the representation of fossil calibrations on bayesian estimation of species divergence times. Syst Biol, 2010, 59: 74-89 CrossRef PubMed Google Scholar

[21] Warnock R C M, Parham J F, Joyce W G, et al. Calibration uncertainty in molecular dating analyses: There is no substitute for the prior evaluation of time priors. Proc R Soc B-Biol Sci, 2015, 282: 20141013 CrossRef PubMed Google Scholar

[22] Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol, 1981, 17: 368-376 CrossRef ADS Google Scholar

[23] Guindon S. Bayesian estimation of divergence times from large sequence alignments. Mol Biol Evol, 2010, 27: 1768-1781 CrossRef PubMed Google Scholar

[24] dos Reis M, Yang Z. Approximate likelihood calculation on a phylogeny for bayesian estimation of divergence times. Mol Biol Evol, 2011, 28: 2161-2172 CrossRef PubMed Google Scholar

[25] Zuckerkandl E, Pauling L. Evolutionary divergence and convergence in proteins. Evol Genes Protein, 1965, 97: 97−166. Google Scholar

[26] Kimura M. Evolutionary rate at the molecular level. J Genet Mol Biol, 1968, 18: 219−225. Google Scholar

[27] King J L, Jukes T H. Non-darwinian evolution. Science, 1969, 164: 788-798 CrossRef ADS Google Scholar

[28] Yang Z H. Computational Molecular Evolution. Oxford: Oxford University Press, 2006. Google Scholar

[29] Langley C H, Fitch W M. An examination of the constancy of the rate of molecular evolution. J Mol Evol, 1974, 3: 161-177 CrossRef ADS Google Scholar

[30] Yoder A D, Yang Z. Estimation of primate speciation dates using local molecular clocks. Mol Biol Evol, 2000, 17: 1081-1090 CrossRef PubMed Google Scholar

[31] Hasegawa M, Thorne J L, Kishino H. Time scale of eutherian evolution estimated without assuming a constant rate of molecular evolution. Genes Genet Syst, 2003, 78: 267-283 CrossRef Google Scholar

[32] Springer M S, Murphy W J, Eizirik E, et al. Placental mammal diversification and the cretaceous-tertiary boundary. Proc Natl Acad Sci USA, 2003, 100: 1056-1061 CrossRef PubMed ADS Google Scholar

[33] Bromham L, Penny D. The modern molecular clock. Nat Rev Genet, 2003, 4: 216-224 CrossRef PubMed Google Scholar

[34] Ho S Y W. The changing face of the molecular evolutionary clock. Trends Ecol Evol, 2014, 29: 496-503 CrossRef PubMed Google Scholar

[35] Kishino H, Hasegawa M. Converting distance to time: Application to human evolution. Methods Enzymol, 1990, 183: 550−570. Google Scholar

[36] Kendall D G. On the Generalized "Birth-and-Death" Process. Ann Math Statist, 1948, 19: 1-15 CrossRef Google Scholar

[37] Yang Z, Rannala B. Bayesian phylogenetic inference using DNA sequences: A markov chain monte carlo method. Mol Biol Evol, 1997, 14: 717-724 CrossRef PubMed Google Scholar

[38] Nee S, May R M, Harvey P H. The reconstructed evolutionary process. Phil Trans R Soc Lond B, 1994, 344: 305-311 CrossRef PubMed Google Scholar

[39] Heath T A, Huelsenbeck J P, Stadler T. The fossilized birth-death process for coherent calibration of divergence-time estimates. Proc Natl Acad Sci USA, 2014, 111: E2957-E2966 CrossRef PubMed ADS arXiv Google Scholar

[40] Donoghue P C J, Benton M J. Rocks and clocks: Calibrating the tree of life using fossils and molecules. Trends Ecol Evol, 2007, 22: 424-431 CrossRef PubMed Google Scholar

[41] Ho S Y W, Phillips M J. Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst Biol, 2009, 58: 367-380 CrossRef PubMed Google Scholar

[42] Goswami A, Upchurch P. The dating game: A reply to heads. Zool Scr, 2010, 39: 406−409. Google Scholar

[43] Graur D, Martin W. Reading the entrails of chickens: Molecular timescales of evolution and the illusion of precision. Trends Genets, 2004, 20: 80-86 CrossRef PubMed Google Scholar

[44] Donoghue P, Benton M, Yang Z H, et al. Calibrating and constraining the molecular clock. J Vertebr Paleontol, 2009, 29: 89a−89a. Google Scholar

[45] Reisz R R, Müller J. Molecular timescales and the fossil record: A paleontological perspective. Trends Genets, 2004, 20: 237-241 CrossRef PubMed Google Scholar

[46] Benton M J, Donoghue P C J. Paleontological evidence to date the tree of life. Mol Biol Evol, 2007, 24: 26-53 CrossRef PubMed Google Scholar

[47] Warnock R C M, Yang Z, Donoghue P C J. Exploring uncertainty in the calibration of the molecular clock. Biol Lett, 2012, 8: 156-159 CrossRef PubMed Google Scholar

[48] Yang Z. Paml 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol, 2007, 24: 1586-1591 CrossRef PubMed Google Scholar

[49] Bouckaert R, Heled J, Kühnert D, et al. Beast 2: A software platform for bayesian evolutionary analysis. PLoS Comput Biol, 2014, 10: e1003537 CrossRef PubMed ADS Google Scholar

[50] Dos Reis M, Zhu T, Yang Z. The impact of the rate prior on bayesian estimation of divergence times with multiple loci. Syst Biol, 2014, 63: 555-565 CrossRef PubMed Google Scholar

[51] Benton M, Donoghue P, Asher R. Calibrating and constraining molecular clocks. In: Near T, ed. The Timetree of Life. New York: Oxford University Press. 2009, 35–86. Google Scholar

[52] Rannala B, Zhu T, Yang Z. Tail paradox, partial identifiability, and influential priors in bayesian branch length inference. Mol Biol Evol, 2012, 29: 325-335 CrossRef PubMed Google Scholar

[53] Zhang C, Rannala B, Yang Z. Robustness of compound dirichlet priors for bayesian inference of branch lengths. Syst Biol, 2012, 61: 779-784 CrossRef PubMed Google Scholar

[54] Jukes T H, Cantor C R. Evolution of protein molecules. Mamm Protein Metab, 1969, 21−132. Google Scholar

[55] Zhu T, Dos Reis M, Yang Z. Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci. Syst Biol, 2015, 64: 267-280 CrossRef PubMed Google Scholar

[56] Ronquist F, Teslenko M, van der Mark P, et al. Mrbayes 3.2: Efficient bayesian phylogenetic inference and model choice across a large model space. Syst Biol, 2012, 61: 539-542 CrossRef PubMed Google Scholar

[57] Ronquist F, Huelsenbeck J P. Mrbayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 2003, 19: 1572-1574 CrossRef Google Scholar

[58] Lartillot N, Lepage T, Blanquart S. Phylobayes 3: A bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics, 2009, 25: 2286-2288 CrossRef PubMed Google Scholar

[59] Lartillot N, Rodrigue N, Stubbs D, et al. Phylobayes mpi: Phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst Biol, 2013, 62: 611-615 CrossRef PubMed Google Scholar

[60] Heath T A, Holder M T, Huelsenbeck J P. A dirichlet process prior for estimating lineage-specific substitution rates. Mol Biol Evol, 2012, 29: 939-955 CrossRef PubMed Google Scholar

  • Figure 1

    Posterior estimation of the human-chimpanzee divergence times under the i.i.d. prior for locus rate. The three rate priors used are (1) A fast rate, μi∼G(2, 2) (diamonds), with prior mean 1 (substitutions per site per 108 years); (2) A medium rate μi∼G(2, 20) (empty circles), with prior mean 0.1; and (3) A slow rate, μi∼G(2, 200) (black circles), with prior mean 0.01. When the prior rate is too fast, the estimated time becomes younger as L is increased. On the other hand, when the prior rate is too slow, the time becomes older with increased L. In both cases, the posterior times are outside the fossil bounds (dashed lines) when L=300 loci are used. The x axis is the number of loci used and the time unit is My

  • Figure 2

    Time prior, rate priors, and time posteriors in the problem of divergence time estimation with fossil calibrations. A: The density of the fossil prior with soft bound 0.112<t<0.337 (100 My). The probabilities that the divergence time is less than 0.113 and larger than 0.337 are 2.5% each. B: The densities of two rate prior: G(1, 10) (solid line) and InvG(2, 0.2) (dash line). Both rate priors are with mean 0.1 (i.e., 10−9 substitutions per site per year) and standard error 0.01. C: The densities of posterior time estimations with rate priors G(1, 10) and InvG(3, 0.2). With both rate priors, the posterior mean is 0.2637 with 95% HPD CI to be (0.1325, 0.3420) (color online)

qqqq

Contact and support