메뉴 건너뛰기




Volumn 55, Issue , 2010, Pages 189-206

Bayesian phylogenetics and its influence on insect systematics

Author keywords

Bayes factor; Markov chain Monte Carlo; Model averaging; Model choice; Molecular evolution

Indexed keywords

HEXAPODA;

EID: 77449143195     PISSN: 00664170     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.ento.54.110807.090529     Document Type: Review
Times cited : (37)

References (98)
  • 1
    • 33847256882 scopus 로고    scopus 로고
    • A step toward barcoding life: A model-based, decision-theoretic method to assign genes to preexisting species groups
    • Abdo Z, Golding GB. 2007. A step toward barcoding life: a model-based, decision-theoretic method to assign genes to preexisting species groups. Syst. Biol. 56:44-56
    • (2007) Syst. Biol. , vol.56 , pp. 44-56
    • Abdo, Z.1    Golding, G.B.2
  • 3
    • 33845381928 scopus 로고    scopus 로고
    • The posterior and the prior in Bayesian phylogenetics
    • Alfaro ME, Holder MT. 2006. The posterior and the prior in Bayesian phylogenetics. Annu. Rev. Ecol. Evol. Syst. 37:19-42
    • (2006) Annu. Rev. Ecol. Evol. Syst. , vol.37 , pp. 19-42
    • Alfaro, M.E.1    Holder, M.T.2
  • 4
    • 1342309210 scopus 로고    scopus 로고
    • Parallel Metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference
    • Altekar G, Dwarkadas S, Huelsenbeck JP, Ronquist F. 2004. Parallel Metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20:407-415
    • (2004) Bioinformatics , vol.20 , pp. 407-415
    • Altekar, G.1    Dwarkadas, S.2    Huelsenbeck, J.P.3    Ronquist, F.4
  • 6
    • 0036804729 scopus 로고    scopus 로고
    • Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny
    • Aris-Brosou S, Yang Z. 2002. Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny. Syst. Biol. 51:703-714
    • (2002) Syst. Biol. , vol.51 , pp. 703-714
    • Aris-Brosou, S.1    Yang, Z.2
  • 7
    • 2442562450 scopus 로고    scopus 로고
    • Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. RECOMB '04: Proc
    • San Diego, March ACM
    • Arvestad L, Berglund AC, Lagergren J, Sennblad B. 2004. Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. RECOMB '04: Proc. 8th Annu. Int. Conf. Res. Comput. Mol. Biol., San Diego, March 27-31. ACM
    • (2004) 8th Annu. Int. Conf. Res. Comput. Mol. Biol. , pp. 27-31
    • Arvestad, L.1    Berglund, A.C.2    Lagergren, J.3    Sennblad, B.4
  • 8
    • 53849128927 scopus 로고    scopus 로고
    • A model-based approach to study nearest-neighbor influences reveals complex substitution patterns in noncoding sequences
    • Baele G, Van de Peer Y, Vansteelandt S. 2008. A model-based approach to study nearest-neighbor influences reveals complex substitution patterns in noncoding sequences. Syst. Biol. 57:675-692
    • (2008) Syst. Biol. , vol.57 , pp. 675-692
    • Baele, G.1    Van De Peer, Y.2    Vansteelandt, S.3
  • 9
    • 33749595631 scopus 로고    scopus 로고
    • A Bayesian compound stochastic process for modeling nonstation-ary and nonhomogeneous sequence evolution
    • Blanquart S, Lartillot N. 2006. A Bayesian compound stochastic process for modeling nonstation-ary and nonhomogeneous sequence evolution. Mol. Biol. Evol. 23:2058-2071
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 2058-2071
    • Blanquart, S.1    Lartillot, N.2
  • 10
    • 47249122561 scopus 로고    scopus 로고
    • A site-and time-heterogeneous model of amino acid replacement
    • Blanquart S, Lartillot N. 2008. A site-and time-heterogeneous model of amino acid replacement. Mol. Biol. Evol. 25:842-858
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 842-858
    • Blanquart, S.1    Lartillot, N.2
  • 11
    • 0035986890 scopus 로고    scopus 로고
    • Bayesian model adequacy and choice in phylogenetics
    • Bollback J. 2002. Bayesian model adequacy and choice in phylogenetics. Mol. Biol. Evol. 19:1171-1180
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 1171-1180
    • Bollback, J.1
  • 12
    • 0032273615 scopus 로고    scopus 로고
    • General methods for monitoring convergence of iterative simulations
    • Brooks SP, Gelman A. 1998. General methods for monitoring convergence of iterative simulations. J. Comput. Graph. Stat. 7:434-455
    • (1998) J. Comput. Graph. Stat. , vol.7 , pp. 434-455
    • Brooks, S.P.1    Gelman, A.2
  • 13
    • 33747338447 scopus 로고    scopus 로고
    • Differentiating between hypotheses of lineage sorting and introgression in New Zealand alpine cicadas (Maoricicada Dugdale)
    • Buckley TR, Cordeiro M, Marshall DC, Simon C. 2006. Differentiating between hypotheses of lineage sorting and introgression in New Zealand alpine cicadas (Maoricicada Dugdale). Syst. Biol. 55:411-425
    • (2006) Syst. Biol. , vol.55 , pp. 411-425
    • Buckley, T.R.1    Cordeiro, M.2    Marshall, D.C.3    Simon, C.4
  • 14
    • 58149269030 scopus 로고    scopus 로고
    • The influence of model averaging on clade posteriors: An example using the triggerfishes (family Balistidae)
    • Dornburg A, Santini F, Alfaro ME. 2008. The influence of model averaging on clade posteriors: an example using the triggerfishes (family Balistidae). Syst. Biol. 57:905-919
    • (2008) Syst. Biol. , vol.57 , pp. 905-919
    • Dornburg, A.1    Santini, F.2    Alfaro, M.E.3
  • 16
    • 0036021407 scopus 로고    scopus 로고
    • Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data
    • Drummond AJ, Nicholls GK, Rodrigo AG, Solomon W. 2002. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161:1307-1320
    • (2002) Genetics , vol.161 , pp. 1307-1320
    • Drummond, A.J.1    Nicholls, G.K.2    Rodrigo, A.G.3    Solomon, W.4
  • 17
    • 38649110663 scopus 로고    scopus 로고
    • BEAST: Bayesian evolutionary analysis by sampling trees
    • Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214
    • (2007) BMC Evol. Biol. , vol.7 , pp. 214
    • Drummond, A.J.1    Rambaut, A.2
  • 18
  • 19
    • 0030034795 scopus 로고    scopus 로고
    • A hidden Markov model approach to variation among sites in rate of evolution
    • Felsenstein J, Churchill GA. 1996. A hidden Markov model approach to variation among sites in rate of evolution. Mol. Biol. Evol. 13:93-104
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 93-104
    • Felsenstein, J.1    Churchill, G.A.2
  • 20
    • 52049118280 scopus 로고    scopus 로고
    • A preliminary mitochondrial genome phylogeny of Orthoptera (Insecta) and approaches to maximizing phylogenetic signal found within mitochondrial genome data
    • Fenn JD, Song H, Cameron SL, Whiting MF. 2008. A preliminary mitochondrial genome phylogeny of Orthoptera (Insecta) and approaches to maximizing phylogenetic signal found within mitochondrial genome data. Mol. Phylogenet. Evol. 49:59-68
    • (2008) Mol. Phylogenet. Evol. , vol.49 , pp. 59-68
    • Fenn, J.D.1    Song, H.2    Cameron, S.L.3    Whiting, M.F.4
  • 21
    • 3242701529 scopus 로고    scopus 로고
    • Modeling compositional heterogeneity
    • Foster PG. 2004. Modeling compositional heterogeneity. Syst. Biol. 53:485-495
    • (2004) Syst. Biol. , vol.53 , pp. 485-495
    • Foster, P.G.1
  • 22
    • 0031829758 scopus 로고    scopus 로고
    • Inferring pattern and process: Maximum-likelihood implementation of a non-homogeneous model of DNA sequence evolution for phylogenetic analysis
    • Galtier N, Gouy M. 1998. Inferring pattern and process: maximum-likelihood implementation of a non-homogeneous model of DNA sequence evolution for phylogenetic analysis. Mol. Biol. Evol. 15:871-879
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 871-879
    • Galtier, N.1    Gouy, M.2
  • 23
    • 0000736067 scopus 로고    scopus 로고
    • Simulating normalizing constants: From importance sampling to bridge sampling to path sampling
    • Gelman A. 1998. Simulating normalizing constants: from importance sampling to bridge sampling to path sampling. Stat. Sci. 13:163-185
    • (1998) Stat. Sci. , vol.13 , pp. 163-185
    • Gelman, A.1
  • 25
    • 12344282043 scopus 로고    scopus 로고
    • A comprehensive analysis of mammalian mitochondrial genome base composition and improved phylogenetic methods
    • Gibson A, Gowri-Shankar V, Higgs PG, Rattray M. 2005. A comprehensive analysis of mammalian mitochondrial genome base composition and improved phylogenetic methods. Mol. Biol. Evol. 22:251-264
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 251-264
    • Gibson, A.1    Gowri-Shankar, V.2    Higgs, P.G.3    Rattray, M.4
  • 26
    • 0031805465 scopus 로고    scopus 로고
    • Assessing the impact of secondary structure and solvent accessibility on protein evolution
    • Goldman N, Thorne JL, Jones DT. 1998. Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics 149:445-458
    • (1998) Genetics , vol.149 , pp. 445-458
    • Goldman, N.1    Thorne, J.L.2    Jones, D.T.3
  • 27
    • 34548074524 scopus 로고    scopus 로고
    • A reversible jump method for Bayesian phylogenetic inference with a nonhomogeneous substitution model
    • Gowri-Shankar V, Rattray M. 2007. A reversible jump method for Bayesian phylogenetic inference with a nonhomogeneous substitution model. Mol. Biol. Evol. 24:1286-1299
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 1286-1299
    • Gowri-Shankar, V.1    Rattray, M.2
  • 28
    • 77956889087 scopus 로고
    • Reversible jump Markov chain Monte Carlo computation and Bayesian model determination
    • Green PJ. 1995. Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82:711-732
    • (1995) Biometrika , vol.82 , pp. 711-732
    • Green, P.J.1
  • 29
    • 0029068893 scopus 로고
    • Maximum likelihood estimation of the heterogeneity of substitution rates among nucleotide sites
    • Gu Y, Fu YX, Lu WH. 1995. Maximum likelihood estimation of the heterogeneity of substitution rates among nucleotide sites. Mol. Biol. Evol. 12:546-557
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 546-557
    • Gu, Y.1    Fu, Y.X.2    Lu, W.H.3
  • 30
    • 14544277657 scopus 로고    scopus 로고
    • Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences
    • Hall BG. 2005. Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences. Mol. Biol. Evol. 22:792-802
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 792-802
    • Hall, B.G.1
  • 31
    • 31344432889 scopus 로고    scopus 로고
    • The promise of DNA barcoding for taxonomy
    • Hebert PDN, Gregory TR. 2005. The promise of DNA barcoding for taxonomy. Syst. Biol. 54:852-859
    • (2005) Syst. Biol. , vol.54 , pp. 852-859
    • Hebert, P.D.N.1    Gregory, T.R.2
  • 32
    • 33846532499 scopus 로고    scopus 로고
    • DNA barcoding will often fail to discover new animal species over broad parameter space
    • Hickerson MJ, Meyer CP, Moritz C. 2006. DNA barcoding will often fail to discover new animal species over broad parameter space. Syst. Biol. 55:729-739
    • (2006) Syst. Biol. , vol.55 , pp. 729-739
    • Hickerson, M.J.1    Meyer, C.P.2    Moritz, C.3
  • 33
    • 57149093199 scopus 로고    scopus 로고
    • Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes
    • Holder MT, Zwickl DJ, Dessimoz C. 2008. Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes. Philos. Trans. R. Soc. B 363:4013-4021
    • (2008) Philos. Trans. R. Soc. , vol.B363 , pp. 4013-4021
    • Holder, M.T.1    Zwickl, D.J.2    Dessimoz, C.3
  • 37
    • 2442671519 scopus 로고    scopus 로고
    • Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo
    • Huelsenbeck JP, Larget B, Alfaro ME. 2004. Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. Mol. Biol. Evol. 21:1123-1133
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1123-1133
    • Huelsenbeck, J.P.1    Larget, B.2    Alfaro, M.E.3
  • 38
    • 0036806280 scopus 로고    scopus 로고
    • Potential applications and pitfalls of Bayesian inference of phylogeny
    • Huelsenbeck JP, Larget B, Miller RE, Ronquist F. 2002. Potential applications and pitfalls of Bayesian inference of phylogeny. Syst. Biol. 51:673-688
    • (2002) Syst. Biol. , vol.51 , pp. 673-688
    • Huelsenbeck, J.P.1    Larget, B.2    Miller, R.E.3    Ronquist, F.4
  • 39
    • 0034077901 scopus 로고    scopus 로고
    • A compound Poisson process for relaxing the molecular clock
    • Huelsenbeck JP, Larget B, Swofford D. 2000. A compound Poisson process for relaxing the molecular clock. Genetics 154:1879-1892
    • (2000) Genetics , vol.154 , pp. 1879-1892
    • Huelsenbeck, J.P.1    Larget, B.2    Swofford, D.3
  • 40
    • 11144277878 scopus 로고    scopus 로고
    • Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models
    • Huelsenbeck JP, Rannala B. 2004. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst. Biol. 53:904-913
    • (2004) Syst. Biol. , vol.53 , pp. 904-913
    • Huelsenbeck, J.P.1    Rannala, B.2
  • 41
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES. Bayesian inferenceof phylogeny
    • Huelsenbeck JP, Ronquist F. 2001. MRBAYES. Bayesian inferenceof phylogeny. Bioinformatics 17:754-755
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 42
    • 0035861456 scopus 로고    scopus 로고
    • Bayesian inference of phylogeny and its impact on evolutionary biology
    • Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-2314
    • (2001) Science , vol.294 , pp. 2310-2314
    • Huelsenbeck, J.P.1    Ronquist, F.2    Nielsen, R.3    Bollback, J.P.4
  • 43
    • 39549117235 scopus 로고    scopus 로고
    • A nonparametric method for accommodating and testing across-site rate variation
    • Huelsenbeck JP, Suchard MA. 2007. A nonparametric method for accommodating and testing across-site rate variation. Syst. Biol. 56:975-987
    • (2007) Syst. Biol. , vol.56 , pp. 975-987
    • Huelsenbeck, J.P.1    Suchard, M.A.2
  • 44
    • 37549050969 scopus 로고    scopus 로고
    • A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation
    • Hunt T, Bergsten J, Levkanicova Z, Papadopoulou A, St John O, et al. 2007. A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation. Science 318:1913-1916
    • (2007) Science , vol.318 , pp. 1913-1916
    • Hunt, T.1    Bergsten, J.2    Levkanicova, Z.3    Papadopoulou, A.4    St John, O.5
  • 45
    • 4644300141 scopus 로고    scopus 로고
    • Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
    • Hwang DG, Green P. 2004. Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc. Natl. Acad. Sci. USA 101:13994-14001
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 13994-14001
    • Hwang, D.G.1    Green, P.2
  • 46
    • 0036728808 scopus 로고    scopus 로고
    • Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution
    • Jow H, Hudelot C, Rattray M, Higgs PG. 2002. Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution. Mol. Biol. Evol. 19:1591-1601
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 1591-1601
    • Jow, H.1    Hudelot, C.2    Rattray, M.3    Higgs, P.G.4
  • 48
    • 35748954378 scopus 로고    scopus 로고
    • Effects of branch length uncertainty on Bayesian posterior probabilities for phylogenetic hypotheses
    • Kolaczkowski B, Thornton JW. 2007. Effects of branch length uncertainty on Bayesian posterior probabilities for phylogenetic hypotheses. Mol. Biol. Evol. 24:2108-2118
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 2108-2118
    • Kolaczkowski, B.1    Thornton, J.W.2
  • 50
    • 0032976397 scopus 로고    scopus 로고
    • Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees
    • Larget B, Simon DL. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phyloge-netic trees. Mol. Biol. Evol. 16:750-759 (Pubitemid 29260829)
    • (1999) Molecular Biology and Evolution , vol.16 , Issue.6 , pp. 750-759
    • Larget, B.1    Simon, D.L.2
  • 51
    • 2442691520 scopus 로고    scopus 로고
    • A Bayesian mixture model for across-site heterogeneities in the amino acid replacement process
    • Lartillot N, Philippe H. 2004. A Bayesian mixture model for across-site heterogeneities in the amino acid replacement process. Mol. Biol. Evol. 21:1095-1109
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1095-1109
    • Lartillot, N.1    Philippe, H.2
  • 52
    • 33644826560 scopus 로고    scopus 로고
    • Computing Bayes factors using thermodynamic integration
    • Lartillot N, Philippe H. 2006. Computing Bayes factors using thermodynamic integration. Syst. Biol. 55:195-207
    • (2006) Syst. Biol. , vol.55 , pp. 195-207
    • Lartillot, N.1    Philippe, H.2
  • 54
    • 34249778653 scopus 로고    scopus 로고
    • Mitonuclear discordance is caused by rampant mitochondrial introgression in Neodiprion (Hymenoptera: Diprionidae) sawflies
    • Linnen CR, Farrell BD. 2007. Mitonuclear discordance is caused by rampant mitochondrial introgression in Neodiprion (Hymenoptera: Diprionidae) sawflies. Evolution 61:1417-1438
    • (2007) Evolution , vol.61 , pp. 1417-1438
    • Linnen, C.R.1    Farrell, B.D.2
  • 55
    • 58149239783 scopus 로고    scopus 로고
    • Comparison of methods for species-tree inference in the sawfly genus Neodiprion (Hymenoptera: Diprionidae)
    • Linnen CR, Farrell BD. 2008. Comparison of methods for species-tree inference in the sawfly genus Neodiprion (Hymenoptera: Diprionidae). Syst. Biol. 57:876-890
    • (2008) Syst. Biol. , vol.57 , pp. 876-890
    • Linnen, C.R.1    Farrell, B.D.2
  • 57
    • 33749535839 scopus 로고    scopus 로고
    • DNA barcoding and taxonomy in Diptera: A tale of high intraspecific variability and low identification success
    • Meier R, Shiyang K, Vaidya G, Ng PKL. 2006. DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Syst. Biol. 55:715-728
    • (2006) Syst. Biol. , vol.55 , pp. 715-728
    • Meier, R.1    Shiyang, K.2    Vaidya, G.3    Ng, P.K.L.4
  • 58
    • 25844516325 scopus 로고    scopus 로고
    • Phylogenetic MCMC algorithms are misleading on mixtures of trees
    • Mossel E, Vigoda E. 2005. Phylogenetic MCMC algorithms are misleading on mixtures of trees. Science 309:2207-2209
    • (2005) Science , vol.309 , pp. 2207-2209
    • Mossel, E.1    Vigoda, E.2
  • 59
    • 33646161941 scopus 로고    scopus 로고
    • Response to comment on "phylogenetic MCMC algorithms are misleading on mixtures of trees"
    • Mossel E, Vigoda E. 2006. Response to comment on "Phylogenetic MCMC algorithms are misleading on mixtures of trees. " Science 312:367
    • (2006) Science , vol.312 , pp. 367
    • Mossel, E.1    Vigoda, E.2
  • 61
    • 0003078723 scopus 로고
    • Approximating Bayesian inference with the weighted likelihood bootstrap
    • Newton MA, Raftery AE. 1994. Approximating Bayesian inference with the weighted likelihood bootstrap. J. R. Stat. Soc. B 56:3-48
    • (1994) J. R. Stat. Soc. , vol.B56 , pp. 3-48
    • Newton, M.A.1    Raftery, A.E.2
  • 62
    • 33644605459 scopus 로고    scopus 로고
    • Statistical approaches for DNA barcoding
    • Nielsen R, Matz M. 2006. Statistical approaches for DNA barcoding. Syst. Biol. 55:162-169
    • (2006) Syst. Biol. , vol.55 , pp. 162-169
    • Nielsen, R.1    Matz, M.2
  • 63
    • 0031972161 scopus 로고    scopus 로고
    • Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    • Nielsen R, Yang Z. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929-936
    • (1998) Genetics , vol.148 , pp. 929-936
    • Nielsen, R.1    Yang, Z.2
  • 65
    • 39149141072 scopus 로고    scopus 로고
    • AWTY(are we there yet?): A system for graphical exploration of MCMC convergence in Bayesian phylogenetics
    • Nylander J, Wilgenbusch J, Warren D. 2008. AWTY(are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24:581-583
    • (2008) Bioinformatics , vol.24 , pp. 581-583
    • Nylander, J.1    Wilgenbusch, J.2    Warren, D.3
  • 66
    • 0000487096 scopus 로고
    • A Monte Carlo method for high dimensional integration
    • Ogata Y. 1989. A Monte Carlo method for high dimensional integration. Num. Math. 55:137-157
    • (1989) Num. Math. , vol.55 , pp. 137-157
    • Ogata, Y.1
  • 67
    • 4243140058 scopus 로고    scopus 로고
    • A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data
    • Pagel M, Meade A. 2004. A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. Syst. Biol. 53:571-581
    • (2004) Syst. Biol. , vol.53 , pp. 571-581
    • Pagel, M.1    Meade, A.2
  • 68
    • 34548444940 scopus 로고    scopus 로고
    • Sequence-based species delimitation for the DNA taxonomy of undescribed insects
    • Pons J, Barraclough TG, Gomez-Zurita J, Cardoso A, Duran DP, et al. 2006. Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst. Biol. 55:595-609
    • (2006) Syst. Biol. , vol.55 , pp. 595-609
    • Pons, J.1    Barraclough, T.G.2    Gomez-Zurita, J.3    Cardoso, A.4    Duran, D.P.5
  • 69
    • 0031773680 scopus 로고    scopus 로고
    • Modeltest: Testing the model ofDNA substitution
    • Posada D, Crandall KA. 1998. Modeltest: testing the model ofDNA substitution. Bioinformatics 14:817-818
    • (1998) Bioinformatics , vol.14 , pp. 817-818
    • Posada, D.1    Crandall, K.A.2
  • 70
    • 0035527410 scopus 로고    scopus 로고
    • Selecting the best-fit modelof nucleotide substitution
    • Posada D, Crandall KA. 2001. Selecting the best-fit modelof nucleotide substitution. Syst. Biol. 50:580-601
    • (2001) Syst. Biol , vol.50 , pp. 580-601
    • Posada, D.1    Crandall, K.A.2
  • 72
    • 0029818407 scopus 로고    scopus 로고
    • Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference
    • Rannala B, Yang Z. 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43:304-311
    • (1996) J. Mol. Evol. , vol.43 , pp. 304-311
    • Rannala, B.1    Yang, Z.2
  • 74
    • 22844450838 scopus 로고    scopus 로고
    • Joint Bayesian estimation of alignment and phylogeny
    • Redelings BD, Suchard MA. 2005. Joint Bayesian estimation of alignment and phylogeny. Syst. Biol. 54:401-418
    • (2005) Syst. Biol. , vol.54 , pp. 401-418
    • Redelings, B.D.1    Suchard, M.A.2
  • 75
    • 58149236596 scopus 로고    scopus 로고
    • Resolving arthropod phylogeny: Exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence
    • Regier J, Shultz J, Ganley A, Hussey A, Shi D, et al. 2008. Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence. Syst. Biol. 57:920-998
    • (2008) Syst. Biol. , vol.57 , pp. 920-998
    • Regier, J.1    Shultz, J.2    Ganley, A.3    Hussey, A.4    Shi, D.5
  • 77
    • 33748126145 scopus 로고    scopus 로고
    • Assessing site-interdependent phylogenetic models of sequence evolution
    • Rodrigue N, Philippe H, Lartillot N. 2006. Assessing site-interdependent phylogenetic models of sequence evolution. Mol. Biol. Evol. 23:1762-1775
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 1762-1775
    • Rodrigue, N.1    Philippe, H.2    Lartillot, N.3
  • 78
    • 0042147779 scopus 로고    scopus 로고
    • Parsimony analysis of coevolving species associations
    • ed. RDM Page Chicago: Univ. Chicago Press
    • Ronquist F. 2002. Parsimony analysis of coevolving species associations. In Tangled Trees: Phylogeny, Cospe-ciation and Coevolution, ed. RDM Page, pp. 22-64. Chicago: Univ. Chicago Press
    • (2002) Tangled Trees: Phylogeny, Cospe-ciation and Coevolution , pp. 22-64
    • Ronquist, F.1
  • 79
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes3: Bayesian phylogenetic inference under mixed models
    • Ronquist F, Huelsenbeck JP. 2003. MrBayes3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 82
    • 28944450584 scopus 로고    scopus 로고
    • Choosing appropriate substitution models for the phylo-genetic analysis of protein-coding sequences
    • Shapiro B, Rambaut A, Drummond AJ. 2006. Choosing appropriate substitution models for the phylo-genetic analysis of protein-coding sequences. Mol. Biol. Evol. 23:7-9
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 7-9
    • Shapiro, B.1    Rambaut, A.2    Drummond, A.J.3
  • 83
    • 14644397888 scopus 로고    scopus 로고
    • RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees
    • DOI 10.1093/bioinformatics/bti191
    • Stamatakis A, Ludwig T, Meier H. 2005. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21:456-463 (Pubitemid 40310232)
    • (2005) Bioinformatics , vol.21 , Issue.4 , pp. 456-463
    • Stamatakis, A.1    Ludwig, T.2    Meier, H.3
  • 84
    • 0242404116 scopus 로고    scopus 로고
    • Hierarchical phylogenetic models for analyzing multipartite sequence data
    • Suchard MA, Kitchen CMR, Sinsheimer JS, Weiss RE. 2003. Hierarchical phylogenetic models for analyzing multipartite sequence data. Syst. Biol. 52:649-664
    • (2003) Syst. Biol. , vol.52 , pp. 649-664
    • Suchard, M.A.1    Kitchen, C.M.R.2    Sinsheimer, J.S.3    Weiss, R.E.4
  • 85
    • 33747863926 scopus 로고    scopus 로고
    • BAli-Phy: Simultaneous Bayesian inference of alignment and phy-logeny
    • Suchard MA, Redelings BD. 2006. BAli-Phy: simultaneous Bayesian inference of alignment and phy-logeny. Bioinformatics 22:2047-2048
    • (2006) Bioinformatics , vol.22 , pp. 2047-2048
    • Suchard, M.A.1    Redelings, B.D.2
  • 86
    • 0034983646 scopus 로고    scopus 로고
    • Bayesian selection of continuous-time Markov chain evolutionary models
    • Suchard MA, Weiss RE, Sinsheimer JS. 2001. Bayesian selection of continuous-time Markov chain evolutionary models. Mol. Biol. Evol. 18:1001-1013
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 1001-1013
    • Suchard, M.A.1    Weiss, R.E.2    Sinsheimer, J.S.3
  • 88
    • 0037058983 scopus 로고    scopus 로고
    • Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics
    • Suzuki Y, Glazko GV, Nei M. 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. USA 99:16138-16143
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 16138-16143
    • Suzuki, Y.1    Glazko, G.V.2    Nei, M.3
  • 89
    • 77952853657 scopus 로고    scopus 로고
    • On estimating topology and divergence times in phylogenetics
    • PhD thesis. Uppsala Univ
    • Svennblad B. 2008. On estimating topology and divergence times in phylogenetics. PhD thesis. Uppsala Univ., Sweden. 52 pp.
    • (2008) Sweden. , pp. 52
    • Svennblad, B.1
  • 91
    • 0026079507 scopus 로고
    • An evolutionary model for maximum likelihood alignment of DNA sequences
    • Thorne JL, Kishino H, Felsenstein J. 1991. An evolutionary model for maximum likelihood alignment of DNA sequences. J. Mol. Evol. 33:114-124
    • (1991) J. Mol. Evol. , vol.33 , pp. 114-124
    • Thorne, J.L.1    Kishino, H.2    Felsenstein, J.3
  • 92
    • 0031741182 scopus 로고    scopus 로고
    • Estimating the rateofevolutionofthe rate ofmolecular evolution
    • Thorne JL, KishinoH, Painter IS. 1998. Estimating the rateofevolutionofthe rate ofmolecular evolution. Mol. Biol. Evol. 15:1647-1657
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 1647-1657
    • Thorne, J.L.1    Kishinohpainter, I.S.2
  • 93
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • Yang Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39:306-314
    • (1994) J. Mol. Evol. , vol.39 , pp. 306-314
    • Yang, Z.1
  • 94
    • 0028813337 scopus 로고
    • A space-time process model for the evolution of DNA sequences
    • Yang Z. 1995. A space-time process model for the evolution of DNA sequences. Genetics 139:993-1005
    • (1995) Genetics , vol.139 , pp. 993-1005
    • Yang, Z.1
  • 95
    • 0029970097 scopus 로고    scopus 로고
    • Maximum-likelihood models for combined analyses of multiple sequence data
    • Yang Z. 1996. Maximum-likelihood models for combined analyses of multiple sequence data. J. Mol. Evol. 42:587-596
    • (1996) J. Mol. Evol. , vol.42 , pp. 587-596
    • Yang, Z.1
  • 96
    • 0030749810 scopus 로고    scopus 로고
    • Bayesian phylogenetic inference using DNA sequences: A Markov Chain Monte Carlo Method
    • Yang Z, Rannala B. 1997. Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method. Mol. Biol. Evol. 14:717-724
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 717-724
    • Yang, Z.1    Rannala, B.2
  • 97
    • 0028961933 scopus 로고
    • On the use of nucleic acid sequences to infer branchings in the tree of life
    • Yang Z, Roberts D. 1995. On the use of nucleic acid sequences to infer branchings in the tree of life. Mol. Biol. Evol. 12:451-458
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 451-458
    • Yang, Z.1    Roberts, D.2
  • 98
    • 12444337674 scopus 로고    scopus 로고
    • Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics
    • Zwickl D, Holder M. 2004. Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics. Syst. Biol. 53:877-888
    • (2004) Syst. Biol. , vol.53 , pp. 877-888
    • Zwickl, D.1    Holder, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.