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Volumn 45, Issue 4, 1996, Pages 546-558

Likelihood-ratio test of monophyly

Author keywords

Likelihood ratio test; Maximum likelihood; Monophyly; Phylogenetic methods; Thylacinus

Indexed keywords

CANIS; DASYURIDAE; MAMMALIA; METATHERIA; THYLACINUS;

EID: 0030311344     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1093/sysbio/45.4.546     Document Type: Article
Times cited : (126)

References (49)
  • 1
    • 0025751614 scopus 로고
    • Molecular phylogeny of the superorder Archonta
    • ADKINS, R. M., AND R. L. HONEYCUTT. 1991. Molecular phylogeny of the superorder Archonta. Proc. Natl. Acad. Sci. USA 88:10317-10321.
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 10317-10321
    • Adkins, R.M.1    Honeycutt, R.L.2
  • 2
    • 38249037452 scopus 로고
    • An empirical investigation of some effects of sparseness in contingency tables
    • AGRESTI, A., AND M. C. YANG. 1987. An empirical investigation of some effects of sparseness in contingency tables. Comput. Stat. Data Anal. 5:9-21.
    • (1987) Comput. Stat. Data Anal. , vol.5 , pp. 9-21
    • Agresti, A.1    Yang, M.C.2
  • 3
    • 11944260743 scopus 로고
    • A molecular test of bat relationships: Monophyly or diphyly?
    • AMMERMAN, L. K., AND D. M. HILLIS. 1992. A molecular test of bat relationships: Monophyly or diphyly? Syst. Biol. 41:222-232.
    • (1992) Syst. Biol. , vol.41 , pp. 222-232
    • Ammerman, L.K.1    Hillis, D.M.2
  • 4
    • 0000812447 scopus 로고
    • A review of Miocene thylacinids (Thylacinidae, Marsupialia), the phylogenetic position of the Thylacinidae and the problem of apriorisms in character analysis
    • (M. Archer, ed.). Royal Zoological Society of New South Wales, Sydney
    • ARCHER, M. 1982. A review of Miocene thylacinids (Thylacinidae, Marsupialia), the phylogenetic position of the Thylacinidae and the problem of apriorisms in character analysis. Pages 445-476 in Carnivorous marsupials (M. Archer, ed.). Royal Zoological Society of New South Wales, Sydney.
    • (1982) Carnivorous Marsupials , pp. 445-476
    • Archer, M.1
  • 5
    • 0026582159 scopus 로고
    • Rejection of the "flying primate" hypothesis by phylogenetic evidence from the e-globin gene
    • BAILEY, W. J., J. L. SLIGHTOM, AND M. GOODMAN. 1992. Rejection of the "flying primate" hypothesis by phylogenetic evidence from the e-globin gene. Science 256:86-89.
    • (1992) Science , vol.256 , pp. 86-89
    • Bailey, W.J.1    Slightom, J.L.2    Goodman, M.3
  • 6
    • 0024147409 scopus 로고
    • Are megabats flying primates? Contrary evidence from a mitochondrial DNA sequence
    • BENNET, S., L. J. ALEXANDER, R. H. CROZIER, AND A. G. MACKINLAY. 1988. Are megabats flying primates? Contrary evidence from a mitochondrial DNA sequence. Aust. J. Biol. Sci. 41:327-332.
    • (1988) Aust. J. Biol. Sci. , vol.41 , pp. 327-332
    • Bennet, S.1    Alexander, L.J.2    Crozier, R.H.3    Mackinlay, A.G.4
  • 8
    • 0028362463 scopus 로고
    • Phylogenetic place of guinea pigs: No support of the rodent-polyphyly hypothesis from maximum-likelihood analyses of multiple protein sequences
    • CAO, Y., J. ADACHI, T.-A. YANO, AND M. HASEGAWA. 1994. Phylogenetic place of guinea pigs: No support of the rodent-polyphyly hypothesis from maximum-likelihood analyses of multiple protein sequences. Mol. Biol. Evol. 11:593-604.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 593-604
    • Cao, Y.1    Adachi, J.2    Yano, T.-A.3    Hasegawa, M.4
  • 9
    • 84989491935 scopus 로고
    • Successive weighting, reliability and evidence
    • CARPENTER, J. 1994. Successive weighting, reliability and evidence. Cladistics 10:215-220.
    • (1994) Cladistics , vol.10 , pp. 215-220
    • Carpenter, J.1
  • 10
    • 0029365975 scopus 로고
    • Toward a characterisation of landscapes of combinatorial optimisation problems, with special reference to the phylogeny problem
    • CHARLESTON, M. 1995. Toward a characterisation of landscapes of combinatorial optimisation problems, with special reference to the phylogeny problem. Comput. Biol. 2:439-450.
    • (1995) Comput. Biol. , vol.2 , pp. 439-450
    • Charleston, M.1
  • 11
    • 0004128472 scopus 로고
    • Cambridge Univ. Press, Cambridge, England
    • EDWARDS, A. W. F. 1972. Likelihood. Cambridge Univ. Press, Cambridge, England.
    • (1972) Likelihood
    • Edwards, A.W.F.1
  • 12
    • 77956887385 scopus 로고
    • Bootstrap confidence intervals for a class of parametric problems
    • EFRON, B. 1985. Bootstrap confidence intervals for a class of parametric problems. Biometrika 72:45-58.
    • (1985) Biometrika , vol.72 , pp. 45-58
    • Efron, B.1
  • 13
    • 0025288758 scopus 로고
    • Chance marsupial relationships
    • FAITH, D. P. 1990. Chance marsupial relationships. Nature 345:393-394.
    • (1990) Nature , vol.345 , pp. 393-394
    • Faith, D.P.1
  • 14
    • 84960612286 scopus 로고
    • Cladistic permutation tests for monophyly and nonmonophyly
    • FAITH, D. P. 1991. Cladistic permutation tests for monophyly and nonmonophyly. Syst. Zool. 40:366-375.
    • (1991) Syst. Zool. , vol.40 , pp. 366-375
    • Faith, D.P.1
  • 15
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • FELSENSTEIN, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17:368-376.
    • (1981) J. Mol. Evol. , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 16
    • 0024152983 scopus 로고
    • Phylogenies from molecular sequences: Inference and reliability
    • FELSENSTEIN, J. 1988. Phylogenies from molecular sequences: Inference and reliability. Annu. Rev. Genet. 22:521-565.
    • (1988) Annu. Rev. Genet. , vol.22 , pp. 521-565
    • Felsenstein, J.1
  • 17
    • 0027526039 scopus 로고
    • Statistical tests of models of DNA substitution
    • GOLDMAN, N. 1993. Statistical tests of models of DNA substitution. J. Mol. Evol. 36:182-198.
    • (1993) J. Mol. Evol. , vol.36 , pp. 182-198
    • Goldman, N.1
  • 18
    • 0024605359 scopus 로고
    • Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree
    • GOUY, M., AND W.-H. LI. 1989. Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree. Science 339:145-147.
    • (1989) Science , vol.339 , pp. 145-147
    • Gouy, M.1    Li, W.-H.2
  • 19
    • 0026428609 scopus 로고
    • Is the guinea-pig a rodent?
    • GRAUER, D., W. A. HIDE, AND W.-H. LI. 1991. Is the guinea-pig a rodent? Nature 351:649-652.
    • (1991) Nature , vol.351 , pp. 649-652
    • Grauer, D.1    Hide, W.A.2    Li, W.-H.3
  • 20
    • 0026550202 scopus 로고
    • The biochemical phylogeny of guinea-pigs and gundis, and the paraphyly of the order Rodentia
    • GRAUER, D., W. A. HIDE, A. ZHARKIKH, AND W.-H. LI. 1992. The biochemical phylogeny of guinea-pigs and gundis, and the paraphyly of the order Rodentia. Comp. Biochem. Physiol. B 101:495-498.
    • (1992) Comp. Biochem. Physiol. B , vol.101 , pp. 495-498
    • Grauer, D.1    Hide, W.A.2    Zharkikh, A.3    Li, W.-H.4
  • 21
    • 0000408645 scopus 로고
    • Log-linear models and frequency tables with small expected cell counts
    • HABERMAN, S. J. 1977. Log-linear models and frequency tables with small expected cell counts. Ann. Stat. 5:1148-1169.
    • (1977) Ann. Stat. , vol.5 , pp. 1148-1169
    • Haberman, S.J.1
  • 23
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • HASEGAWA, M., H. KISHINO, AND T. YANO. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 21:160-174.
    • (1985) J. Mol. Evol. , vol.21 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 24
    • 11944268967 scopus 로고
    • Performance of phylogenetic methods in simulation
    • HUELSENBECK, J. P. 1995a. Performance of phylogenetic methods in simulation. Syst. Biol. 44:17-48.
    • (1995) Syst. Biol. , vol.44 , pp. 17-48
    • Huelsenbeck, J.P.1
  • 25
    • 0029113744 scopus 로고
    • The robustness of two phylogenetic methods: Four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining
    • HUELSENBECK, J. P. 1995b. The robustness of two phylogenetic methods: Four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining. Mol. Biol. Evol. 12:843-849.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 843-849
    • Huelsenbeck, J.P.1
  • 26
    • 0030328811 scopus 로고    scopus 로고
    • A likelihood ratio test to detect conflicting phylogenetic signal
    • HUELSENBECK, J. P., AND J. J. BULL. 1996. A likelihood ratio test to detect conflicting phylogenetic signal. Syst. Biol. 45:92-98.
    • (1996) Syst. Biol. , vol.45 , pp. 92-98
    • Huelsenbeck, J.P.1    Bull, J.J.2
  • 27
    • 0002410257 scopus 로고    scopus 로고
    • Parametric bootstrapping in molecular phylogenetics: Applications and performance
    • (J. D. Ferraris and S. R. Palumbi, eds.). Wiley & Sons, New York
    • HUELSENBECK, J. P., D. M. HILLIS, AND R. JONES. 1996. Parametric bootstrapping in molecular phylogenetics: Applications and performance. Pages 19-45 in Molecular zoology: Advances, strategies and protocols (J. D. Ferraris and S. R. Palumbi, eds.). Wiley & Sons, New York.
    • (1996) Molecular Zoology: Advances, Strategies and Protocols , pp. 19-45
    • Huelsenbeck, J.P.1    Hillis, D.M.2    Jones, R.3
  • 28
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • (H. Munro, ed.). Academic Press, New York
    • JUKES, T. H., AND C. R. CANTOR. 1969. Evolution of protein molecules. Pages 21-132 in Mammalian protein metabolism (H. Munro, ed.). Academic Press, New York.
    • (1969) Mammalian Protein Metabolism , pp. 21-132
    • Jukes, T.H.1    Cantor, C.R.2
  • 29
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences
    • KIMURA, M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
    • (1980) J. Mol. Evol. , vol.16 , pp. 111-120
    • Kimura, M.1
  • 30
    • 0024307824 scopus 로고
    • Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea
    • KISHINO, H., AND M. HASEGAWA. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29: 170-179.
    • (1989) J. Mol. Evol. , vol.29 , pp. 170-179
    • Kishino, H.1    Hasegawa, M.2
  • 31
    • 0028177080 scopus 로고
    • A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates
    • KUHNER, M. K., AND J. FELSENSTEIN. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11:459-468.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 459-468
    • Kuhner, M.K.1    Felsenstein, J.2
  • 32
    • 0027483517 scopus 로고
    • Structure and evolution of opossum, guinea pig, and porcupine cytochrome b genes
    • MA, D.-P., A. ZHARKIKH, D. GRAUER, J. L. VANDEBERG, AND W.-H. LI. 1993. Structure and evolution of opossum, guinea pig, and porcupine cytochrome b genes. J. Mol. Evol. 36:327-334.
    • (1993) J. Mol. Evol. , vol.36 , pp. 327-334
    • Ma, D.-P.1    Zharkikh, A.2    Grauer, D.3    VandeBerg, J.L.4    Li, W.-H.5
  • 34
    • 0025887478 scopus 로고
    • Phylogenetic relationships among megabats, microbats and primates
    • MINDELL, D. P., C. W. DICK, AND R. J. BAKER. 1991. Phylogenetic relationships among megabats, microbats and primates. Proc. Natl. Acad. Sci. USA 88: 10322-10326.
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 10322-10326
    • Mindell, D.P.1    Dick, C.W.2    Baker, R.J.3
  • 35
    • 0022461702 scopus 로고
    • Flying primates? Megabats have the advanced pathway from eye to midbrain
    • PETTIGREW, J. D. 1986. Flying primates? Megabats have the advanced pathway from eye to midbrain. Science 231:1304-1306.
    • (1986) Science , vol.231 , pp. 1304-1306
    • Pettigrew, J.D.1
  • 36
    • 0000993093 scopus 로고
    • Wings or brain? Convergent evolution in the origins of bats
    • PETTIGREW, J. D. 1991. Wings or brain? Convergent evolution in the origins of bats. Syst. Zool. 40:199-216.
    • (1991) Syst. Zool. , vol.40 , pp. 199-216
    • Pettigrew, J.D.1
  • 38
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • ROBINSON, D. F., AND L. R. FOULDS. 1981. Comparison of phylogenetic trees. Math. Biosci. 53:131-147.
    • (1981) Math. Biosci. , vol.53 , pp. 131-147
    • Robinson, D.F.1    Foulds, L.R.2
  • 40
    • 0026870120 scopus 로고
    • A molecular perspective on mammalian evolution from the gene encoding interphotoreceptor retinoid binding protein, with convincing evidence for bat monophyly
    • STANHOPE, M. J., J. CZELUSNIAK, J.-S. SI, J. NICKERSON, AND M. GOODMAN. 1992. A molecular perspective on mammalian evolution from the gene encoding interphotoreceptor retinoid binding protein, with convincing evidence for bat monophyly. Mol. Phylogenet. Evol. 1:148-160.
    • (1992) Mol. Phylogenet. Evol. , vol.1 , pp. 148-160
    • Stanhope, M.J.1    Czelusniak, J.2    Si, J.-S.3    Nickerson, J.4    Goodman, M.5
  • 42
    • 0030310653 scopus 로고    scopus 로고
    • The topology-dependent permutation test for monophyly does not test for monophyly
    • SWOFFORD, D. L., J. L. THORNE, J. FELSENSTEIN, AND B. M. WIEGMANN. 1996. The topology-dependent permutation test for monophyly does not test for monophyly. Syst. Biol. 45:575-579.
    • (1996) Syst. Biol. , vol.45 , pp. 575-579
    • Swofford, D.L.1    Thorne, J.L.2    Felsenstein, J.3    Wiegmann, B.M.4
  • 43
    • 0028205953 scopus 로고
    • Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site
    • TATENO, Y., N. TAKEZAKI, AND M. NEI. 1994. Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site. Mol. Biol. Evol. 11: 261-277.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 261-277
    • Tateno, Y.1    Takezaki, N.2    Nei, M.3
  • 44
    • 0021084212 scopus 로고
    • Phylogenetic inference from restriction site endonuclease cleavage site maps with particular reference to the humans and apes
    • TEMPLETON, A. R. 1983. Phylogenetic inference from restriction site endonuclease cleavage site maps with particular reference to the humans and apes. Evolution 37:221-244.
    • (1983) Evolution , vol.37 , pp. 221-244
    • Templeton, A.R.1
  • 45
    • 0024856302 scopus 로고
    • DNA phylogeny of the extinct marsupial wolf
    • THOMAS, R. H., W. SCHAFFNER, A. C. WILSON, AND S. PÄÄBO. 1989. DNA phylogeny of the extinct marsupial wolf. Nature 340:465-167.
    • (1989) Nature , vol.340 , pp. 465-1167
    • Thomas, R.H.1    Schaffner, W.2    Wilson, A.C.3    Pääbo, S.4
  • 46
    • 0002574561 scopus 로고    scopus 로고
    • Evolutionary trees of apes and humans from DNA sequences
    • (A. J. Lock and C. R. Peters, eds.). Oxford Univ. Press, Oxford, England
    • WADDELL, P. J., AND D. PENNY. 1996. Evolutionary trees of apes and humans from DNA sequences. Pages 53-73 in Handbook of symbolic evolution (A. J. Lock and C. R. Peters, eds.). Oxford Univ. Press, Oxford, England
    • (1996) Handbook of Symbolic Evolution , pp. 53-73
    • Waddell, P.J.1    Penny, D.2
  • 47
    • 0027132974 scopus 로고
    • Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
    • YANG, Z. 1993. Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10:1396-1401.
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 1396-1401
    • Yang, Z.1
  • 48
    • 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
  • 49
    • 0028267146 scopus 로고
    • Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation
    • YANG, Z., N. GOLDMAN, AND A. FRIDAY. 1994. Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol. Biol. Evol. 11:316-324.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 316-324
    • Yang, Z.1    Goldman, N.2    Friday, A.3


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