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Volumn 50, Issue 4, 2001, Pages 525-539

Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; COMPARATIVE STUDY; EPIDEMIOLOGY; PHYLOGENY; STATISTICAL MODEL; STATISTICS;

EID: 0035527406     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/106351501750435086     Document Type: Review
Times cited : (329)

References (32)
  • 1
    • 0032927161 scopus 로고    scopus 로고
    • Topological bias and inconsistency of maximum likelihood using wrong models
    • BRUNO, W. J., AND A. L. HALPERN. 1999. Topological bias and inconsistency of maximum likelihood using wrong models. Mol. Biol. Evol. 16:564-566.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 564-566
    • Bruno, W.J.1    Halpern, A.L.2
  • 2
    • 0029919254 scopus 로고    scopus 로고
    • Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters
    • CHANG, J. T. 1996a. Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters. Math. Biosci. 134:189-215.
    • (1996) Math. Biosci. , vol.134 , pp. 189-215
    • Chang, J.T.1
  • 3
    • 0030588055 scopus 로고    scopus 로고
    • Full reconstruction of Markov models on evolutionary trees: Identifiability and consistency
    • CHANG, J. T. 1996b. Full reconstruction of Markov models on evolutionary trees: Identifiability and consistency. Math. Biosci. 137:51-73.
    • (1996) Math. Biosci. , vol.137 , pp. 51-73
    • Chang, J.T.1
  • 4
    • 0001151063 scopus 로고
    • The logical basis of phylogenetic analysis
    • (N. I. Platnick and V. A. Funk, eds.). Columbia Univ. Press, New York
    • FARRIS, J. S. 1983. The logical basis of phylogenetic analysis. Pages 7-36 in Advances in cladistics, Volume 2 (N. I. Platnick and V. A. Funk, eds.). Columbia Univ. Press, New York.
    • (1983) Advances in Cladistics , vol.2 , pp. 7-36
    • Farris, J.S.1
  • 5
    • 0040459974 scopus 로고    scopus 로고
    • Who, really is a statistician?
    • George Washington Univ. Washington, DC
    • FARRIS, J. S. 1997. "Who, really is a statistician?" Paper presented at the Sixteenth Meeting of the Willi Hennig Society. George Washington Univ. Washington, DC.
    • (1997) Sixteenth Meeting of the Willi Hennig Society
    • Farris, J.S.1
  • 6
    • 0000074814 scopus 로고    scopus 로고
    • Likelihood and inconsistency
    • FARRIS, J. S. 1999. Likelihood and inconsistency. Cladistics 15:199-204.
    • (1999) Cladistics , vol.15 , pp. 199-204
    • Farris, J.S.1
  • 7
    • 0030417648 scopus 로고    scopus 로고
    • Parsimony jackknifing outperforms neighbor-joining
    • FARRIS, J. S., V. A. ALBERT, D. LIPSCOMB, AND A. G. Kluge. 1996. Parsimony jackknifing outperforms neighbor-joining. Cladistics 12:99-124.
    • (1996) Cladistics , vol.12 , pp. 99-124
    • Farris, J.S.1    Albert, V.A.2    Lipscomb, D.3    Kluge, A.G.4
  • 8
    • 84959798530 scopus 로고
    • Cases in which parsimony and compatibility methods will be positively misleading
    • FELSENSTEIN, J. 1978. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
    • (1978) Syst. Zool. , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 9
    • 0000461280 scopus 로고
    • Confidence limits on phylogenies: An approach using the bootstrap
    • FELSENSTEIN, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
    • (1985) Evolution , vol.39 , pp. 783-791
    • Felsenstein, J.1
  • 10
    • 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
  • 11
    • 0028887457 scopus 로고
    • Success of maximum likelihood in the four-taxon case
    • GAUT, B. S., AND P. O. LEWIS. 1995. Success of maximum likelihood in the four-taxon case. Mol. Biol. Evol. 12:152-162.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 152-162
    • Gaut, B.S.1    Lewis, P.O.2
  • 12
    • 0000084234 scopus 로고
    • A framework for the quantitative study of evolutionary trees
    • HENDY, M. D., and D. PENNY. 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:297-309.
    • (1989) Syst. Zool. , vol.38 , pp. 297-309
    • Hendy, M.D.1    Penny, D.2
  • 14
    • 11944268967 scopus 로고
    • Performance of phylogenetic methods in simulation
    • HUELSENBECK, J. 1995. Performance of phylogenetic methods in simulation. Syst. Biol. 44:17-48.
    • (1995) Syst. Biol. , vol.44 , pp. 17-48
    • Huelsenbeck, J.1
  • 15
    • 12044255023 scopus 로고
    • Success of phylogenetic methods in the four-taxon case
    • HUELSENBECK, J. P., AND D. M. HILLIS. 1993. Success of phylogenetic methods in the four-taxon case. Syst. Zool. 42:247-264.
    • (1993) Syst. Zool. , vol.42 , pp. 247-264
    • Huelsenbeck, J.P.1    Hillis, D.M.2
  • 16
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • (H. N. 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. N. Munro, ed.). Academic Press, New York.
    • (1969) Mammalian Protein Metabolism , pp. 21-132
    • Jukes, T.H.1    Cantor, C.R.2
  • 18
    • 0030315308 scopus 로고    scopus 로고
    • General inconsistency conditions for maximum parsimony: Effects of branch lengths and increasing numbers of taxa
    • KIM, J. 1996. General inconsistency conditions for maximum parsimony: Effects of branch lengths and increasing numbers of taxa. Syst. Biol. 45:363-374.
    • (1996) Syst. Biol. , vol.45 , pp. 363-374
    • Kim, J.1
  • 19
    • 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
  • 20
    • 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
  • 21
    • 0029935637 scopus 로고    scopus 로고
    • Evolution of chlorophyll and bacteriochlorophyll: The problem of invariant sites in sequence analysis
    • LOCKHART, P. J., A. W. LARKUM, M. A. STEEL, P. J. WADDELL, AND D. PENNY. 1996. Evolution of chlorophyll and bacteriochlorophyll: The problem of invariant sites in sequence analysis. Proc. Natl. Acad. Sci. USA 93:1930-1934.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 1930-1934
    • Lockhart, P.J.1    Larkum, A.W.2    Steel, M.A.3    Waddell, P.J.4    Penny, D.5
  • 22
    • 0022472311 scopus 로고
    • Estimating the reliability of evolutionary trees
    • PENNY, D., AND M. D. HENDY. 1986. Estimating the reliability of evolutionary trees. Mol. Biol. Evol. 3:403-417.
    • (1986) Mol. Biol. Evol. , vol.3 , pp. 403-417
    • Penny, D.1    Hendy, M.D.2
  • 23
    • 0031284363 scopus 로고    scopus 로고
    • On the consistency of maximum likelihood estimation of phylogenetic trees from nucleotide sequences
    • ROGERS, J. S. 1997. On the consistency of maximum likelihood estimation of phylogenetic trees from nucleotide sequences. Syst. Biol. 46:354-357.
    • (1997) Syst. Biol. , vol.46 , pp. 354-357
    • Rogers, J.S.1
  • 24
    • 0000215283 scopus 로고    scopus 로고
    • Success of parsimony in the four-taxon case: Long-branch repulsion by likelihood in the Farris zone
    • SIDDALL, M. E. 1998. Success of parsimony in the four-taxon case: Long-branch repulsion by likelihood in the Farris zone. Cladistics 14:209-220.
    • (1998) Cladistics , vol.14 , pp. 209-220
    • Siddall, M.E.1
  • 25
    • 0344430832 scopus 로고    scopus 로고
    • Probabilism and phylogenetic inference
    • SIDDALL, M. E., AND A. G. KLUGE. 1997. Probabilism and phylogenetic inference. Cladistics 13:313-336.
    • (1997) Cladistics , vol.13 , pp. 313-336
    • Siddall, M.E.1    Kluge, A.G.2
  • 26
    • 0028766117 scopus 로고
    • Parsimony or statistics?
    • SIDOW, A. 1994. Parsimony or statistics? Nature 367:26-27.
    • (1994) Nature , vol.367 , pp. 26-27
    • Sidow, A.1
  • 27
    • 0002618746 scopus 로고    scopus 로고
    • Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics
    • SULLIVAN, J., AND D. L. SWOFFORD. 1997. Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics. J. Mammal. Evol. 4:77-86.
    • (1997) J. Mammal. Evol. , vol.4 , pp. 77-86
    • Sullivan, J.1    Swofford, D.L.2
  • 28
    • 0040459973 scopus 로고
    • The phylogenetic utility of LogDet/paralinear distances for more realistic evolutionary models. I. Is there a heavy price for using them when a simpler model would suffice?
    • Montreal, Canada
    • SWOFFORD, D. L., P. O. LEWIS, AND F. J. WADDELL. 1995. "The phylogenetic utility of LogDet/paralinear distances for more realistic evolutionary models. I. Is there a heavy price for using them when a simpler model would suffice?" Paper presented at annual meeting of the Society for the Study of Evolution/Society of Systematic Biologists, Montreal, Canada.
    • (1995) Annual Meeting of the Society for the Study of Evolution/Society of Systematic Biologists
    • Swofford, D.L.1    Lewis, P.O.2    Waddell, P.J.3
  • 30
    • 0031202202 scopus 로고    scopus 로고
    • Hadamard conjugations and modeling sequence evolution with unequal rates across sites
    • WADDELL, P. J., D. PENNY, AND T. MOORE. 1997. Hadamard conjugations and modeling sequence evolution with unequal rates across sites. Mol. Phylogenet. Evol. 8:33-50.
    • (1997) Mol. Phylogenet. Evol. , vol.8 , pp. 33-50
    • Waddell, P.J.1    Penny, D.2    Moore, T.3
  • 31
    • 0000167944 scopus 로고
    • Note on the consistency of maximum likelihood
    • WALD, A. 1949. Note on the consistency of maximum likelihood. Ann. Math. Stat. 20:595-601.
    • (1949) Ann. Math. Stat. , vol.20 , pp. 595-601
    • Wald, A.1
  • 32
    • 0029878719 scopus 로고    scopus 로고
    • Phylogenetic analysis using parsimony and likelihood methods
    • YANG, Z. 1996. Phylogenetic analysis using parsimony and likelihood methods. J. Mol. Evol. 42:294-307.
    • (1996) J. Mol. Evol. , vol.42 , pp. 294-307
    • Yang, Z.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.