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Volumn 27, Issue 9, 2010, Pages 1988-1999

Robustness of ancestral sequence reconstruction to phylogenetic uncertainty

Author keywords

ancestral state reconstruction; Bayesian; gene reconstruction; maximum likelihood; phylogenetic analysis; simulation

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ANCESTRAL SEQUENCE RECONSTRUCTION; ARTICLE; BAYES THEOREM; GENE SEQUENCE; MAXIMUM LIKELIHOOD METHOD; PHYLOGENETIC TREE CONSTRUCTION METHOD; PHYLOGENY; UNCERTAINTY;

EID: 77955975654     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msq081     Document Type: Article
Times cited : (123)

References (40)
  • 1
    • 10944228197 scopus 로고    scopus 로고
    • Reconstructing large regions of an ancestral mammalian genome in silico
    • Blanchette M, Green ED, Miller W, Haussler D. 2004. Reconstructing large regions of an ancestral mammalian genome in silico. Genome Res. 14:2412-2423
    • (2004) Genome Res. , vol.14 , pp. 2412-2423
    • Blanchette, M.1    Green, E.D.2    Miller, W.3    Haussler, D.4
  • 2
    • 33645691679 scopus 로고    scopus 로고
    • Evolution of hormone-receptor complexity by molecular exploitation
    • Bridgham JT, Carroll SM, Thornton JW. 2006. Evolution of hormone-receptor complexity by molecular exploitation. Science 307: 97-101
    • (2006) Science , vol.307 , pp. 97-101
    • Bridgham, J.T.1    Carroll, S.M.2    Thornton, J.W.3
  • 4
    • 34548018528 scopus 로고    scopus 로고
    • Mechanistic approaches to the study of evolution: The functional synthesis
    • Dean AM, Thornton JW. 2007. Mechanistic approaches to the study of evolution: the functional synthesis. Nat Rev Genet. 8(9):675-688
    • (2007) Nat Rev Genet. , vol.8 , Issue.9 , pp. 675-688
    • Dean, A.M.1    Thornton, J.W.2
  • 5
    • 0003991673 scopus 로고    scopus 로고
    • Sunderland (MA) Sinauer Associates Gaucher EA, Govindarajan S, Ganesh OK. 2007
    • Felsenstein J. 2004. Inferring phylogenies. Sunderland (MA): Sinauer Associates.
    • (2004) Inferring Phylogenies
    • Felsenstein, J.1
  • 6
    • 38949093003 scopus 로고    scopus 로고
    • Palaeotemperature trend for precambrian life inferred from resurrected proteins
    • Gaucher EA, Govindarajan S, Ganesh OK. 2007. Palaeotemperature trend for precambrian life inferred from resurrected proteins. Nature 451:704-707
    • (2007) Nature , vol.451 , pp. 704-707
    • Gaucher, E.A.1    Govindarajan, S.2    Ganesh, O.K.3
  • 7
    • 0141828152 scopus 로고    scopus 로고
    • Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins
    • Gaucher EA, Thomson JM, Burgan MF, Benner SA. 2003. Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature 425(18):285-288
    • (2003) Nature , vol.425 , Issue.18 , pp. 285-288
    • Gaucher, E.A.1    Thomson, J.M.2    Burgan, M.F.3    Benner, S.A.4
  • 8
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52(5):696-704
    • (2003) Syst Biol. , vol.52 , Issue.5 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 9
    • 47749095118 scopus 로고    scopus 로고
    • Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees
    • Heath TA, Zwickl DJ, Kim J, Hillis DM. 2008. Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees. Syst Biol. 57(1):160-166
    • (2008) Syst Biol. , vol.57 , Issue.1 , pp. 160-166
    • Heath, T.A.1    Zwickl, D.J.2    Kim, J.3    Hillis, D.M.4
  • 10
    • 0032023889 scopus 로고    scopus 로고
    • Taxonomic sampling, phylogenetic accuracy, and investigator bias
    • Hillis DM. 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst Biol. 47(1):3-8
    • (1998) Syst Biol. , vol.47 , Issue.1 , pp. 3-8
    • Hillis, D.M.1
  • 11
    • 0035527347 scopus 로고    scopus 로고
    • Empirical and hierarchical Bayesian estimation of ancestral states
    • Huelsenbeck JP, Bollback JP. 2001. Empirical and hierarchical Bayesian estimation of ancestral states. Syst Biol. 50(3):351-366
    • (2001) Syst Biol. , vol.50 , Issue.3 , pp. 351-366
    • Huelsenbeck, J.P.1    Bollback, J.P.2
  • 12
    • 0028895702 scopus 로고
    • Reconstructing the evolutionary history of the artiodactyl ribonuclease superfam-ily
    • Jermann TM, Opitz JG, Stackhouse J, Benner SA. 1995. Reconstructing the evolutionary history of the artiodactyl ribonuclease superfam-ily. 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
  • 13
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones DT, Taylor WR, Thornton JM. 1991. The rapid generation of mutation data matrices from protein sequences. Bioinformatics 8(3):275-282
    • (1991) Bioinformatics , vol.8 , Issue.3 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 14
    • 0038420019 scopus 로고    scopus 로고
    • Molecular basis and evolutionary origins of color diversity in great star coral montastraea cavernosa (scleractinia: Faviida)
    • Kelmanson IV, Matz MV. 2003. Molecular basis and evolutionary origins of color diversity in great star coral montastraea cavernosa (scleractinia: Faviida). Mol Biol Evol. 20(7):1125-1133
    • (2003) Mol Biol Evol. , vol.20 , Issue.7 , pp. 1125-1133
    • Kelmanson, I.V.1    Matz, M.V.2
  • 15
    • 7244221755 scopus 로고    scopus 로고
    • Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous
    • Kolaczkowski B, Thornton JW. 2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431(7011):980-984
    • (2004) Nature , vol.431 , Issue.7011 , pp. 980-984
    • Kolaczkowski, B.1    Thornton, J.W.2
  • 16
    • 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(9):2108-2118
    • (2007) Mol Biol Evol. , vol.24 , Issue.9 , pp. 2108-2118
    • Kolaczkowski, B.1    Thornton, J.W.2
  • 17
    • 44649184070 scopus 로고    scopus 로고
    • A mixed branch length model of heterotachy improves phylogenetic accuracy
    • Kolaczkowski B, Thornton JW. 2008. A mixed branch length model of heterotachy improves phylogenetic accuracy. Mol Biol Evol. 25(6):1054-1066
    • (2008) Mol Biol Evol. , vol.25 , Issue.6 , pp. 1054-1066
    • Kolaczkowski, B.1    Thornton, J.W.2
  • 18
    • 77949525939 scopus 로고    scopus 로고
    • Long-branch attraction bias and inconsistency in Bayesian phylogenetics
    • Kolaczkowski B, Thornton JW. 2009. Long-branch attraction bias and inconsistency in Bayesian phylogenetics. PLoS One 4(12): e7891.
    • (2009) PLoS One , vol.4 , Issue.12
    • Kolaczkowski, B.1    Thornton, J.W.2
  • 19
    • 0029881442 scopus 로고    scopus 로고
    • Probabilistic reconstruction of ancestral protein sequences
    • Koshi JM, Goldstein RA. 1996. Probabilistic reconstruction of ancestral protein sequences. J Mol Evol. 42:313-320
    • (1996) J Mol Evol. , vol.42 , pp. 313-320
    • Koshi, J.M.1    Goldstein, R.A.2
  • 20
    • 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(6):1095-1109
    • (2004) Mol Biol Evol. , vol.21 , Issue.6 , pp. 1095-1109
    • Lartillot, N.1    Philippe, H.2
  • 21
    • 84870718483 scopus 로고    scopus 로고
    • Liberles D, editor New York: Oxford University Press
    • Liberles D, editor. 2007. Ancestral sequence reconstruction. New York: Oxford University Press.
    • (2007) Ancestral Sequence Reconstruction
  • 22
    • 25144501916 scopus 로고    scopus 로고
    • Counterexample to a claim about the reconstruction of ancestral character states
    • Lucena B, Haussler D. 2005. Counterexample to a claim about the reconstruction of ancestral character states. Syst Biol. 54(4): 693-695
    • (2005) Syst Biol. , vol.54 , Issue.4 , pp. 693-695
    • Lucena, B.1    Haussler, D.2
  • 23
    • 34548040966 scopus 로고    scopus 로고
    • Crystal structure of an ancient protein: Evolution by conformational epis-tasis
    • Ortlund EA, Bridgham JT, Redinbo MR, Thornton JW. 2007. Crystal structure of an ancient protein: evolution by conformational epis-tasis. Science 317(5844):1544-1548
    • (2007) Science , vol.317 , Issue.5844 , pp. 1544-1548
    • Ortlund, E.A.1    Bridgham, J.T.2    Redinbo, M.R.3    Thornton, J.W.4
  • 24
    • 9744245452 scopus 로고    scopus 로고
    • Bayesian estimation of ancestral character states on phylogenies
    • Pagel M, Meade A, Barker D. 2004. Bayesian estimation of ancestral character states on phylogenies. Syst Biol. 53(5):673-684
    • (2004) Syst Biol. , vol.53 , Issue.5 , pp. 673-684
    • Pagel, M.1    Meade, A.2    Barker, D.3
  • 25
    • 0002725360 scopus 로고
    • Chemical paleogenetics: Molecular "restoration studies" of extinct forms of life
    • Pauling L, Zuckerkandl E. 1963. Chemical paleogenetics: molecular "restoration studies" of extinct forms of life. Acta Chem Scand. A(17):S9-S16
    • (1963) Acta Chem Scand. A , vol.17
    • Pauling, L.1    Zuckerkandl, E.2
  • 26
    • 0036699885 scopus 로고    scopus 로고
    • Increased taxon sampling is advantageous for phylogenetic inference
    • Pollock DD, Zwickl DJ, McGuirec JA, Hillis DM. 2002. Increased taxon sampling is advantageous for phylogenetic inference. Syst Biol. 51(4):664-671
    • (2002) Syst Biol. , vol.51 , Issue.4 , pp. 664-671
    • Pollock, D.D.1    Zwickl, D.J.2    McGuirec, J.A.3    Hillis, D.M.4
  • 27
    • 0035348056 scopus 로고    scopus 로고
    • The effect of branch length variation on the selection of models of molecular evolution
    • Posada D. 2001. The effect of branch length variation on the selection of models of molecular evolution. J Mol Evol. 52(5):434-444
    • (2001) J Mol Evol. , vol.52 , Issue.5 , pp. 434-444
    • Posada, D.1
  • 28
    • 0034117082 scopus 로고    scopus 로고
    • A fast algorithm for joint reconstruction of ancestral amino acid sequences
    • Pupko T, Shamir IPR, Graur D. 2000. A fast algorithm for joint reconstruction of ancestral amino acid sequences. Mol Biol Evol. 17(6):890-896
    • (2000) Mol Biol Evol. , vol.17 , Issue.6 , pp. 890-896
    • Pupko, T.1    Ipr, S.2    Graur, D.3
  • 29
    • 0030928378 scopus 로고    scopus 로고
    • Seq-gen: An application for the monte carlo simulation of DNA sequence evolution along phylogenetic trees
    • Rambaut A, Grassly NC. 1997. Seq-gen: an application for the monte carlo simulation of DNA sequence evolution along phylogenetic trees. Bioinformatics 13(3):235-238
    • (1997) Bioinformatics , vol.13 , Issue.3 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 30
    • 29344441657 scopus 로고    scopus 로고
    • Animal evolution and the molecular signature of radiations compressed in time
    • Rokas A, Krüger D, Carroll SB. 2005. Animal evolution and the molecular signature of radiations compressed in time. Science 310(5756):1933-1938
    • (2005) Science , vol.310 , Issue.5756 , pp. 1933-1938
    • Rokas, A.1    Krüger, D.2    Carroll, S.B.3
  • 31
    • 0033432230 scopus 로고    scopus 로고
    • The role of subjectivity in reconstructing ancestral character states: A Bayesian approach to unknown rates, states, and transformation asymmetries
    • Schultz TR, Churchill GA. 1999. The role of subjectivity in reconstructing ancestral character states: a Bayesian approach to unknown rates, states, and transformation asymmetries. Syst Biol. 48(3): 651-664
    • (1999) Syst Biol. , vol.48 , Issue.3 , pp. 651-664
    • Schultz, T.R.1    Churchill, G.A.2
  • 32
    • 0038261973 scopus 로고    scopus 로고
    • Molecular analysis of the evolutionary significance of ultraviolet vision in vertebrates
    • Shi Y, Yokoyama S. 2004. Molecular analysis of the evolutionary significance of ultraviolet vision in vertebrates. Proc Natl Acad Sci\USA. 100(14):8308-8313
    • (2004) Proc Natl Acad Sci\USA. , vol.100 , Issue.14 , pp. 8308-8313
    • Shi, Y.1    Yokoyama, S.2
  • 34
    • 1942531303 scopus 로고    scopus 로고
    • Resurrecting ancient genes: Experimental analysis of extinct molecules
    • Thornton JW. 2004. Resurrecting ancient genes: experimental analysis of extinct molecules. Nature 5:366-375
    • (2004) Nature , vol.5 , pp. 366-375
    • Thornton, J.W.1
  • 35
    • 0141431993 scopus 로고    scopus 로고
    • Resurrecting the ancestral steroid receptor: Ancient origin of estrogen signaling
    • Thornton JW, Need E, Crews D. 2003. Resurrecting the ancestral steroid receptor: ancient origin of estrogen signaling. Science 301(5640):1714-1717
    • (2003) Science , vol.301 , Issue.5640 , pp. 1714-1717
    • Thornton, J.W.1    Need, E.2    Crews, D.3
  • 36
    • 19244366496 scopus 로고    scopus 로고
    • Evolution of coral pigments recreated
    • Ugalde JA, Change BSW, Matz MV. 2004. Evolution of coral pigments recreated. Science 305:1433-1433
    • (2004) Science , vol.305 , pp. 1433-1433
    • Ugalde, J.A.1    Bsw, C.2    Matz, M.V.3
  • 37
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Bioinformatics 13(5):555-556
    • (1997) Bioinformatics , vol.13 , Issue.5 , pp. 555-556
    • Yang, Z.1
  • 38
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24(8):1586-1591
    • (2007) Mol. Biol. Evol. , vol.24 , Issue.8 , pp. 1586-1591
    • Yang, Z.1
  • 39
    • 0028820333 scopus 로고
    • A new method of inference of ancestral nucleotide and amino acid sequences
    • Yang Z, Kumar S, Nei M. 1995. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641-1650
    • (1995) Genetics , vol.141 , pp. 1641-1650
    • Yang, Z.1    Kumar, S.2    Nei, M.3
  • 40
    • 0031025677 scopus 로고    scopus 로고
    • Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods
    • Zhang J, Nei M. 1997. Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods. J Mol Evol. 44(1 Suppl):S139-S146
    • (1997) J Mol Evol. , vol.44 , Issue.1 SUPPL.
    • Zhang, J.1    Nei, M.2


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