使用基因组数据进行贝叶斯物种分化时间估计
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摘要
随着测序技术的发展,基因组数据呈井喷式增长.大量的基因组数据使得我们可以非常准确的估计出进化距离,即进化速率和物种分化时间的乘积.在很多情况下,我们想要了解的是物种分化的绝对时间.然而分子数据并没有分别提供进化速率和分化时间的信息,我们可以使用贝叶斯方法借助化石、先验等外部信息进行估计.近年来,进化模型和计算方法方面研究取得的进展使得我们可以在复杂模型下分析多基因数据.能够分析复杂模型的贝叶斯MCMC方法也成为了主流的物种分化时间估计方法.本文主要介绍贝叶斯物种分化时间估计的框架以及相关工作近年来的进展.
With the advancement of the sequencing technology,the amount of genome data increases explosively.Genome data enable us to estimate the evolutionary distance accurately,which is the product of divergence time and evolutionary rate.However,molecular data do not provide the information about times and rates separately.By combining prior information about times and rates,fossil calibrations which provide information about absolute times,and information from molecular data,Bayesian MCMC methods make it possible to estimate the absolute divergence time as well as the evolutionary rate.With the development of phylogenetic models and computational methods in recent years,multiple loci data can be analyzed under complex models.Nowadays,Bayesian methods have become the prevailing dating methods.In this article,we introduce the framework of Bayesian dating,and the progress made in the related area.
With the advancement of the sequencing technology,the amount of genome data increases explosively.Genome data enable us to estimate the evolutionary distance accurately,which is the product of divergence time and evolutionary rate.However,molecular data do not provide the information about times and rates separately.By combining prior information about times and rates,fossil calibrations which provide information about absolute times,and information from molecular data,Bayesian MCMC methods make it possible to estimate the absolute divergence time as well as the evolutionary rate.With the development of phylogenetic models and computational methods in recent years,multiple loci data can be analyzed under complex models.Nowadays,Bayesian methods have become the prevailing dating methods.In this article,we introduce the framework of Bayesian dating,and the progress made in the related area.
引文
1 Xia X,Yang Q.A distance-based least-square method for dating speciation events.Mol Phylogenet Evol,2011,59:342-353
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
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
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
5 Ho S Y W,Duchêne S.Molecular-clock methods for estimating evolutionary rates and timescales.Mol Ecol,2014,23:5947-5965
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
7 Drummond A J,Ho S Y W,Phillips M J,et al.Relaxed phylogenetics and dating with confidence.PLo S Biol,2006,4:e88
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
9 Lepage T,Bryant D,Philippe H,et al.A general comparison of relaxed molecular clock models.Mol Biol Evol,2007,24:2669-2680
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
11 Thorne J L,Kishino H.Divergence time and evolutionary rate estimation with multilocus data.Syst Biol,2002,51:689-702
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
13 Rannala B,Yang Z.Inferring speciation times under an episodic molecular clock.Syst Biol,2007,56:453-466
14 Stadler T.Sampling-through-time in birth-death trees.J Theor Biol,2010,267:396-404
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
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
17 Donoghue P C J,Yang Z.The evolution of methods for establishing evolutionary timescales.Phil Trans R Soc B,2016,371:20160020
18 Britton T.Estimating divergence times in phylogenetic trees without a molecular clock.Syst Biol,2005,54:500-507
19 Dos Reis M,Yang Z.The unbearable uncertainty of bayesian divergence time estimation.J Syst Evol,2013,51:30-43
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
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
22 Felsenstein J.Evolutionary trees from DNA sequences:A maximum likelihood approach.J Mol Evol,1981,17:368-376
23 Guindon S.Bayesian estimation of divergence times from large sequence alignments.Mol Biol Evol,2010,27:1768-1781
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
25 Zuckerkandl E,Pauling L.Evolutionary divergence and convergence in proteins.Evol Genes Protein,1965,97:97-166
26 Kimura M.Evolutionary rate at the molecular level.J Genet Mol Biol,1968,18:219-225
27 King J L,Jukes T H.Non-darwinian evolution.Science,1969,164:788-798
28 Yang Z H.Computational Molecular Evolution.Oxford:Oxford University Press,2006
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
30 Yoder A D,Yang Z.Estimation of primate speciation dates using local molecular clocks.Mol Biol Evol,2000,17:1081-1090
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
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
33 Bromham L,Penny D.The modern molecular clock.Nat Rev Genet,2003,4:216-224
34 Ho S Y W.The changing face of the molecular evolutionary clock.Trends Ecol Evol,2014,29:496-503
35 Kishino H,Hasegawa M.Converting distance to time:Application to human evolution.Methods Enzymol,1990,183:550-570
36 Kendall D G.On the Generalized"Birth-and-Death"Process.Ann Math Statist,1948,19:1-15
37 Yang Z,Rannala B.Bayesian phylogenetic inference using DNA sequences:A markov chain monte carlo method.Mol Biol Evol,1997,14:717-724
38 Nee S,May R M,Harvey P H.The reconstructed evolutionary process.Phil Trans R Soc Lond B,1994,344:305-311
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
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
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
42 Goswami A,Upchurch P.The dating game:A reply to heads.Zool Scr,2010,39:406-409
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
44 Donoghue P,Benton M,Yang Z H,et al.Calibrating and constraining the molecular clock.J Vertebr Paleontol,2009,29:89a-89a
45 Reisz R R,Müller J.Molecular timescales and the fossil record:A paleontological perspective.Trends Genets,2004,20:237-241
46 Benton M J,Donoghue P C J.Paleontological evidence to date the tree of life.Mol Biol Evol,2007,24:26-53
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
48 Yang Z.Paml 4:Phylogenetic analysis by maximum likelihood.Mol Biol Evol,2007,24:1586-1591
49 Bouckaert R,Heled J,Kühnert D,et al.Beast 2:A software platform for bayesian evolutionary analysis.PLo S Comput Biol,2014,10:e1003537
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
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
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
53 Zhang C,Rannala B,Yang Z.Robustness of compound dirichlet priors for bayesian inference of branch lengths.Syst Biol,2012,61:779-784
54 Jukes T H,Cantor C R.Evolution of protein molecules.Mamm Protein Metab,1969,21-132
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
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
57 Ronquist F,Huelsenbeck J P.Mrbayes 3:Bayesian phylogenetic inference under mixed models.Bioinformatics,2003,19:1572-1574
58 Lartillot N,Lepage T,Blanquart S.Phylobayes 3:A bayesian software package for phylogenetic reconstruction and molecular dating.Bioinformatics,2009,25:2286-2288
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
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
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
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
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
5 Ho S Y W,Duchêne S.Molecular-clock methods for estimating evolutionary rates and timescales.Mol Ecol,2014,23:5947-5965
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
7 Drummond A J,Ho S Y W,Phillips M J,et al.Relaxed phylogenetics and dating with confidence.PLo S Biol,2006,4:e88
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
9 Lepage T,Bryant D,Philippe H,et al.A general comparison of relaxed molecular clock models.Mol Biol Evol,2007,24:2669-2680
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
11 Thorne J L,Kishino H.Divergence time and evolutionary rate estimation with multilocus data.Syst Biol,2002,51:689-702
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
13 Rannala B,Yang Z.Inferring speciation times under an episodic molecular clock.Syst Biol,2007,56:453-466
14 Stadler T.Sampling-through-time in birth-death trees.J Theor Biol,2010,267:396-404
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
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
17 Donoghue P C J,Yang Z.The evolution of methods for establishing evolutionary timescales.Phil Trans R Soc B,2016,371:20160020
18 Britton T.Estimating divergence times in phylogenetic trees without a molecular clock.Syst Biol,2005,54:500-507
19 Dos Reis M,Yang Z.The unbearable uncertainty of bayesian divergence time estimation.J Syst Evol,2013,51:30-43
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
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
22 Felsenstein J.Evolutionary trees from DNA sequences:A maximum likelihood approach.J Mol Evol,1981,17:368-376
23 Guindon S.Bayesian estimation of divergence times from large sequence alignments.Mol Biol Evol,2010,27:1768-1781
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
25 Zuckerkandl E,Pauling L.Evolutionary divergence and convergence in proteins.Evol Genes Protein,1965,97:97-166
26 Kimura M.Evolutionary rate at the molecular level.J Genet Mol Biol,1968,18:219-225
27 King J L,Jukes T H.Non-darwinian evolution.Science,1969,164:788-798
28 Yang Z H.Computational Molecular Evolution.Oxford:Oxford University Press,2006
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
30 Yoder A D,Yang Z.Estimation of primate speciation dates using local molecular clocks.Mol Biol Evol,2000,17:1081-1090
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
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
33 Bromham L,Penny D.The modern molecular clock.Nat Rev Genet,2003,4:216-224
34 Ho S Y W.The changing face of the molecular evolutionary clock.Trends Ecol Evol,2014,29:496-503
35 Kishino H,Hasegawa M.Converting distance to time:Application to human evolution.Methods Enzymol,1990,183:550-570
36 Kendall D G.On the Generalized"Birth-and-Death"Process.Ann Math Statist,1948,19:1-15
37 Yang Z,Rannala B.Bayesian phylogenetic inference using DNA sequences:A markov chain monte carlo method.Mol Biol Evol,1997,14:717-724
38 Nee S,May R M,Harvey P H.The reconstructed evolutionary process.Phil Trans R Soc Lond B,1994,344:305-311
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
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
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
42 Goswami A,Upchurch P.The dating game:A reply to heads.Zool Scr,2010,39:406-409
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
44 Donoghue P,Benton M,Yang Z H,et al.Calibrating and constraining the molecular clock.J Vertebr Paleontol,2009,29:89a-89a
45 Reisz R R,Müller J.Molecular timescales and the fossil record:A paleontological perspective.Trends Genets,2004,20:237-241
46 Benton M J,Donoghue P C J.Paleontological evidence to date the tree of life.Mol Biol Evol,2007,24:26-53
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
48 Yang Z.Paml 4:Phylogenetic analysis by maximum likelihood.Mol Biol Evol,2007,24:1586-1591
49 Bouckaert R,Heled J,Kühnert D,et al.Beast 2:A software platform for bayesian evolutionary analysis.PLo S Comput Biol,2014,10:e1003537
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
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
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
53 Zhang C,Rannala B,Yang Z.Robustness of compound dirichlet priors for bayesian inference of branch lengths.Syst Biol,2012,61:779-784
54 Jukes T H,Cantor C R.Evolution of protein molecules.Mamm Protein Metab,1969,21-132
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
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
57 Ronquist F,Huelsenbeck J P.Mrbayes 3:Bayesian phylogenetic inference under mixed models.Bioinformatics,2003,19:1572-1574
58 Lartillot N,Lepage T,Blanquart S.Phylobayes 3:A bayesian software package for phylogenetic reconstruction and molecular dating.Bioinformatics,2009,25:2286-2288
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
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