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Volumn 53, Issue 5, 2004, Pages 673-684

Bayesian estimation of ancestral character states on phylogenies

Author keywords

Ancestral states; Comparative methods; Maximum likelihood; MCMC; Phylogeny

Indexed keywords

RIBONUCLEASE;

EID: 9744245452     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150490522232     Document Type: Article
Times cited : (973)

References (37)
  • 1
    • 0033442555 scopus 로고    scopus 로고
    • Some limitations of ancestral character-state reconstruction when testing evolutionary hypotheses
    • Cunningham, C. 1999. Some limitations of ancestral character-state reconstruction when testing evolutionary hypotheses. Syst. Biol. 48:665-674.
    • (1999) Syst. Biol. , vol.48 , pp. 665-674
    • Cunningham, C.1
  • 2
    • 0004128472 scopus 로고
    • The Johns Hopkins University Press
    • Edwards, A. W. F. 1972. Likelihood. The Johns Hopkins University Press.
    • (1972) Likelihood
    • Edwards, A.W.F.1
  • 3
    • 0030581603 scopus 로고    scopus 로고
    • Bootstrap confidence levels for phylogenetic trees
    • Efron, B., E. Halloran, and S. Holmes. 1996. Bootstrap confidence levels for phylogenetic trees. Proc. Natl. Acad. Sci. USA 93:13429-13434.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 13429-13434
    • Efron, B.1    Halloran, E.2    Holmes, S.3
  • 4
    • 12044259827 scopus 로고
    • Is there something wrong with the bootstrap? A reply to Hillis and Bull
    • Felsenstein, J., and H. Kishino. 1993. Is there something wrong with the bootstrap? A reply to Hillis and Bull. Syst. Biol. 42:193-200.
    • (1993) Syst. Biol. , vol.42 , pp. 193-200
    • Felsenstein, J.1    Kishino, H.2
  • 5
    • 0033534584 scopus 로고    scopus 로고
    • A nonhyperthermophilic common ancestor to extant life forms
    • Galtier, N., N. Tourasse, and M. Gouy. 1999. A nonhyperthermophilic common ancestor to extant life forms. Science 283:220-221.
    • (1999) Science , vol.283 , pp. 220-221
    • Galtier, N.1    Tourasse, N.2    Gouy, M.3
  • 6
    • 84972511893 scopus 로고
    • Practical Markov chain Monte Carlo
    • Geyer, C. J. 1992. Practical Markov chain Monte Carlo. Stat. Sci. 7:473-511.
    • (1992) Stat. Sci. , vol.7 , pp. 473-511
    • Geyer, C.J.1
  • 7
    • 0002517089 scopus 로고    scopus 로고
    • Introducing Markov chain Monte Carlo
    • (W. R. Gilks, S. Richardson, and D. J. Spiegelhalter, eds.). Chapman and Hall, London
    • Gilks, W. R., S. Richardson, and D. J. Spiegelhalter. 1996. Introducing Markov chain Monte Carlo. Pages 1-19 in Markov Chain Monte Carlo in Practice (W. R. Gilks, S. Richardson, and D. J. Spiegelhalter, eds.). Chapman and Hall, London.
    • (1996) Markov Chain Monte Carlo in Practice , pp. 1-19
    • Gilks, W.R.1    Richardson, S.2    Spiegelhalter, D.J.3
  • 8
    • 0037955994 scopus 로고    scopus 로고
    • Molecular and morphological phylogenies of Ruminantia, and the alternative position of the Moschidae
    • Hassanin, A., and E. J. P. Douzery 2003. Molecular and morphological phylogenies of Ruminantia, and the alternative position of the Moschidae. Syst. Biol. 52:206-228.
    • (2003) Syst. Biol. , vol.52 , pp. 206-228
    • Hassanin, A.1    Douzery, E.J.P.2
  • 9
    • 77956890234 scopus 로고
    • Monte Carlo sampling methods using Markov chains and their applications
    • Hastings, W. 1970. Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57:97-109.
    • (1970) Biometrika , vol.57 , pp. 97-109
    • Hastings, W.1
  • 10
    • 0034727081 scopus 로고    scopus 로고
    • Evolutionary instability of ectomycorrhizal symbioses in basidiomycetes
    • Hibbett D. S., L. B. Gilbert, and M. J. Donoghue. 2000. Evolutionary instability of ectomycorrhizal symbioses in basidiomycetes. Nature 407:506-508.
    • (2000) Nature , vol.407 , pp. 506-508
    • Hibbett, D.S.1    Gilbert, L.B.2    Donoghue, M.J.3
  • 11
    • 53149118259 scopus 로고    scopus 로고
    • Bantu language trees reflect the spread of farming across sub-Saharan Africa: A maximum-parsimony analysis
    • Holden, C. J. 2002. Bantu language trees reflect the spread of farming across sub-Saharan Africa: A maximum-parsimony analysis. Proc. R. Soc. Lond. B 269:793-799.
    • (2002) Proc. R. Soc. Lond. B , vol.269 , pp. 793-799
    • Holden, C.J.1
  • 12
    • 0035527347 scopus 로고    scopus 로고
    • Empirical and hierarchical Bayesian estimation of ancestral states
    • Huelsenbeck, J. P., and J. P. Bollback. 2001. Empirical and hierarchical Bayesian estimation of ancestral states. Syst. Biol. 50:351-366.
    • (2001) Syst. Biol. , vol.50 , pp. 351-366
    • Huelsenbeck, J.P.1    Bollback, J.P.2
  • 13
    • 0035861456 scopus 로고    scopus 로고
    • Bayesian inference of phylogeny and its impact on evolutionary biology
    • Huelsenbeck, J. P., F. Ronquist, R. Nielsen, and J. P. Bollback. 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
  • 14
    • 0028895702 scopus 로고
    • Reconstructing the evolutionary history of the artiodactyl ribonulcease superfamily
    • Jermann, T. M., J. G. Opitz, J. Stackhouse, and S. A. Benner. 1995. Reconstructing the evolutionary history of the artiodactyl ribonulcease superfamily. Nature 374:57-59.
    • (1995) Nature , vol.374 , pp. 57-59
    • Jermann, T.M.1    Opitz, J.G.2    Stackhouse, J.3    Benner, S.A.4
  • 15
    • 0032976397 scopus 로고    scopus 로고
    • Markov chain monte carlo algorithms for the Bayesian analysis of phylogenetic trees
    • Larget, B., and D. L. Simon. 1999. Markov chain monte carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16:750-759.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 750-759
    • Larget, B.1    Simon, D.L.2
  • 16
    • 0035527396 scopus 로고    scopus 로고
    • A likelihood approach to estimating phylogeny from discrete morphological character data
    • Lewis, P. O. 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 50:913-925.
    • (2001) Syst. Biol. , vol.50 , pp. 913-925
    • Lewis, P.O.1
  • 17
    • 0035927638 scopus 로고    scopus 로고
    • Major fungal lineages derived from lichen-symbiotic ancestors
    • Lutzoni, F., M. Pagel, and V. Reeb. 2001. Major fungal lineages derived from lichen-symbiotic ancestors. Nature 411:937-940.
    • (2001) Nature , vol.411 , pp. 937-940
    • Lutzoni, F.1    Pagel, M.2    Reeb, V.3
  • 18
    • 0032906031 scopus 로고    scopus 로고
    • Bayesian phylogenetic inference via Markov chain Monte Carlo methods
    • Mau, B., M. Newton, and B. Larget. 1999. Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics 55:1-12.
    • (1999) Biometrics , vol.55 , pp. 1-12
    • Mau, B.1    Newton, M.2    Larget, B.3
  • 20
    • 0033422612 scopus 로고    scopus 로고
    • Support for one and two rate models of discrete trait evolution
    • Mooers, A. Ø., and D. Schluter. 1999. Support for one and two rate models of discrete trait evolution. Syst. Biol. 48:623-633.
    • (1999) Syst. Biol. , vol.48 , pp. 623-633
    • Mooers, A.Ø.1    Schluter, D.2
  • 21
    • 33746439442 scopus 로고    scopus 로고
    • Bootstrapping phylogenies: Large deviations and dispersion effects
    • Newton, M. 1996. Bootstrapping phylogenies: Large deviations and dispersion effects. Biometrika 83:315-328.
    • (1996) Biometrika , vol.83 , pp. 315-328
    • Newton, M.1
  • 22
    • 0001021240 scopus 로고    scopus 로고
    • Markov chain Monte Carlo for the Bayesian analysis of evolutionary trees from aligned molecular sequences
    • (F. Seillier-Moseiwitch, T. P. Speed, and M. Waterman, eds.). Institute of Mathematical Statistics, Cambridge, UK
    • Newton, M., B. Mau, and B. Larget. 1999. Markov chain Monte Carlo for the Bayesian analysis of evolutionary trees from aligned molecular sequences. Pages 143-162 in Statistics in molecular biology (F. Seillier-Moseiwitch, T. P. Speed, and M. Waterman, eds.). Institute of Mathematical Statistics, Cambridge, UK.
    • (1999) Statistics in Molecular Biology , pp. 143-162
    • Newton, M.1    Mau, B.2    Larget, B.3
  • 23
    • 0036804625 scopus 로고    scopus 로고
    • Mapping mutations on phylogenies
    • Nielsen, R. 2002. Mapping mutations on phylogenies. Syst. Biol. 51:729-739.
    • (2002) Syst. Biol. , vol.51 , pp. 729-739
    • Nielsen, R.1
  • 24
    • 0028097770 scopus 로고
    • Detecting correlated evolution on phylogenies: A general method for the comparative analysis of discrete characters
    • Pagel, M. 1994. Detecting correlated evolution on phylogenies: A general method for the comparative analysis of discrete characters. Proc. R. Soc. B 255:37-45.
    • (1994) Proc. R. Soc. B , vol.255 , pp. 37-45
    • Pagel, M.1
  • 25
    • 0031421806 scopus 로고    scopus 로고
    • Inferring evolutionary processes from phylogenies
    • Pagel, M. 1997. Inferring evolutionary processes from phylogenies. Zool. Scripta 26:331-348.
    • (1997) Zool. Scripta , vol.26 , pp. 331-348
    • Pagel, M.1
  • 26
    • 0033613376 scopus 로고    scopus 로고
    • Inferring the historical patterns of biological evolution
    • Pagel, M. 1999a. Inferring the historical patterns of biological evolution. Nature 401:877-884.
    • (1999) Nature , vol.401 , pp. 877-884
    • Pagel, M.1
  • 27
    • 0033422611 scopus 로고    scopus 로고
    • The maximum likelihood approach to reconstructing ancestral character states on phylogenies
    • Pagel, M. 1999b. The maximum likelihood approach to reconstructing ancestral character states on phylogenies. Syst. Biol. 48:612-622.
    • (1999) Syst. Biol. , vol.48 , pp. 612-622
    • Pagel, M.1
  • 28
    • 0000176247 scopus 로고    scopus 로고
    • Accounting for phylogenetic uncertainty in comparative studies of evolution and adaptation
    • (M. Lässig and A. Valleriani, eds.). Springer-Verlag, Berlin
    • Pagel, M., and F. Lutzoni. 2002. Accounting for phylogenetic uncertainty in comparative studies of evolution and adaptation. Pages 148-161 in Biological evolution and statistical physics (M. Lässig and A. Valleriani, eds.). Springer-Verlag, Berlin.
    • (2002) Biological Evolution and Statistical Physics , pp. 148-161
    • Pagel, M.1    Lutzoni, F.2
  • 29
    • 4243140058 scopus 로고    scopus 로고
    • A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data
    • Pagel, M., and A. Meade. 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
  • 30
    • 33745729042 scopus 로고    scopus 로고
    • Bayesian estimation of correlated evolution across cultures: A case study of marriage systems and wealth transfer at marriage
    • In press. To appear (R. Mace, C.J. Holden, and S. Shennan, eds.). University College London Press, London
    • Pagel, M., and A. Meade. In press. Bayesian estimation of correlated evolution across cultures: A case study of marriage systems and wealth transfer at marriage. To appear in The evolution of cultural diversity: A phylogenetic approach (R. Mace, C.J. Holden, and S. Shennan, eds.). University College London Press, London.
    • The Evolution of Cultural Diversity: A Phylogenetic Approach
    • Pagel, M.1    Meade, A.2
  • 31
    • 0029818407 scopus 로고    scopus 로고
    • Probability distributions of molecular evolutionary trees: A new method of phylogenetic inference
    • Rannala, B., and Z. Yang. 1996. Probability distributions 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
  • 32
    • 0029149610 scopus 로고
    • Uncertainty in ancient phylogenies
    • Schluter, D. 1995. Uncertainty in ancient phylogenies. Nature 377:108-109.
    • (1995) Nature , vol.377 , pp. 108-109
    • Schluter, D.1
  • 33
    • 0031417707 scopus 로고    scopus 로고
    • Likelihood of ancestor states in adaptive radiation
    • Schluter, D., T. Price, A. Ø. Mooers, and D. Ludwig. 1997. Likelihood of ancestor states in adaptive radiation. Evolution 51:1699-1711.
    • (1997) Evolution , vol.51 , pp. 1699-1711
    • Schluter, D.1    Price, T.2    Mooers, A.Ø.3    Ludwig, D.4
  • 34
    • 0001336205 scopus 로고    scopus 로고
    • Phylogenetic inference
    • (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer, Sunderland, Massachusetts
    • Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogenetic inference. Pages 407-514 in Molecular systematics, 2nd edition (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer, Sunderland, Massachusetts.
    • (1996) Molecular Systematics, 2nd Edition , pp. 407-514
    • Swofford, D.L.1    Olsen, G.J.2    Waddell, P.J.3    Hillis, D.M.4
  • 35
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The CLUSTAL X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 36
    • 0031669749 scopus 로고    scopus 로고
    • Genealogical inference from microsatellite data
    • Wilson, I., and D. Balding. 1998. Genealogical inference from microsatellite data. Genetics 150:499-510.
    • (1998) Genetics , vol.150 , pp. 499-510
    • Wilson, I.1    Balding, D.2
  • 37
    • 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


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