메뉴 건너뛰기




Volumn 54, Issue 5, 2005, Pages 731-742

Can incomplete taxa rescue phylogenetic analyses from long-branch attraction?

Author keywords

Combining data; Fossils; Incomplete taxa; Missing data; Phylogenetic accuracy; Simulations; Taxon sampling

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; COMPARATIVE STUDY; COMPUTER SIMULATION; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; SAMPLE SIZE;

EID: 30344464074     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1080/10635150500234583     Document Type: Article
Times cited : (225)

References (45)
  • 1
    • 0037329391 scopus 로고    scopus 로고
    • Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence
    • Alfaro, M. E., S. Zoller, and F. Lutzoni. 2003. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol. Biol. Evol. 20:255-266.
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 255-266
    • Alfaro, M.E.1    Zoller, S.2    Lutzoni, F.3
  • 2
    • 0035527497 scopus 로고    scopus 로고
    • The phylogenetic trunk: Maximal inclusion of taxa with missing data in an analysis of the Lepospondyli (Vertebrata, Tetrapoda)
    • Anderson, J. S. 2001. The phylogenetic trunk: Maximal inclusion of taxa with missing data in an analysis of the Lepospondyli (Vertebrata, Tetrapoda). Syst. Biol. 50:170-193.
    • (2001) Syst. Biol. , vol.50 , pp. 170-193
    • Anderson, J.S.1
  • 4
    • 0023108274 scopus 로고
    • The importance of fossils in elucidating seed plant phylogeny and macroevolution
    • Doyle, J. A., and M. J. Donoghue. 1987. The importance of fossils in elucidating seed plant phylogeny and macroevolution. Rev. Palaeobot. Palynol. 50:63-95.
    • (1987) Rev. Palaeobot. Palynol. , vol.50 , pp. 63-95
    • Doyle, J.A.1    Donoghue, M.J.2
  • 5
    • 0027501821 scopus 로고
    • Taxonomic congruence versus total evidence, and the phylogeny of amniotes inferred from fossils, molecules and morphology
    • Eernisse, D. J., and A. G. Kluge. 1993. Taxonomic congruence versus total evidence, and the phylogeny of amniotes inferred from fossils, molecules and morphology. Mol. Biol. Evol. 10:1170-1195.
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 1170-1195
    • Eernisse, D.J.1    Kluge, A.G.2
  • 6
    • 84959798530 scopus 로고
    • Cases in which parsimony or compatibility methods will be positively misleading
    • Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
    • (1978) Syst. Zool. , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 7
    • 0038785934 scopus 로고    scopus 로고
    • Combined support for wholesale taxic atavism in gavialine crocodylians
    • Gatesy, J., G. Amato, M. Norell, R. DeSalle, and C. Hayashi. 2003. Combined support for wholesale taxic atavism in gavialine crocodylians. Syst. Biol. 52:403-422.
    • (2003) Syst. Biol. , vol.52 , pp. 403-422
    • Gatesy, J.1    Amato, G.2    Norell, M.3    DeSalle, R.4    Hayashi, C.5
  • 8
    • 0028887457 scopus 로고
    • The success of maximum likelihood in the four-taxon case
    • Gaut, B. S., and P. O. Lewis. 1995. The 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
  • 9
    • 0024258114 scopus 로고
    • Amniote phylogeny and the importance of fossils
    • Gauthier, J., A. G. Kluge, and T. Rowe. 1988. Amniote phylogeny and the importance of fossils. Cladistics 4:105-209.
    • (1988) Cladistics , vol.4 , pp. 105-209
    • Gauthier, J.1    Kluge, A.G.2    Rowe, T.3
  • 10
    • 0032025857 scopus 로고    scopus 로고
    • Is it better to add taxa or characters to a difficult phylogenetic problem?
    • Graybeal, A. 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol. 47:9-17.
    • (1998) Syst. Biol. , vol.47 , pp. 9-17
    • Graybeal, A.1
  • 11
    • 0022376704 scopus 로고
    • Dating the human-ape spit by a molecular clock of mitochondrial DNA
    • Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating the human-ape spit by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
    • (1985) J. Mol. Evol. , vol.22 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 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
  • 13
    • 0029834661 scopus 로고    scopus 로고
    • Inferring complex phylogenies
    • Hillis, D. M. 1996. Inferring complex phylogenies. Nature 383:130-131.
    • (1996) Nature , vol.383 , pp. 130-131
    • Hillis, D.M.1
  • 14
    • 0032023889 scopus 로고    scopus 로고
    • Taxonomic sampling, phylogenetic accuracy, and investigator bias
    • Hillis, D. M. 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47:3-8.
    • (1998) Syst. Biol. , vol.47 , pp. 3-8
    • Hillis, D.M.1
  • 15
    • 0242669921 scopus 로고    scopus 로고
    • Is sparse taxon sampling a problem for phylogenetic inference?
    • Hillis, D. M., D. D. Pollock, J. A. McGuire, and D. J. Zwickl. 2003. Is sparse taxon sampling a problem for phylogenetic inference? Syst. Biol. 52:124-126.
    • (2003) Syst. Biol. , vol.52 , pp. 124-126
    • Hillis, D.M.1    Pollock, D.D.2    McGuire, J.A.3    Zwickl, D.J.4
  • 16
    • 84960586331 scopus 로고
    • When are fossils better than extant taxa in phylogenetic analysis?
    • Huelsenbeck, J. P. 1991. When are fossils better than extant taxa in phylogenetic analysis? Syst. Zool. 40:458-469.
    • (1991) Syst. Zool. , vol.40 , pp. 458-469
    • Huelsenbeck, J.P.1
  • 17
    • 11944268967 scopus 로고
    • The performance of phylogenetic methods in simulation
    • Huelsenbeck, J. P. 1995. The performance of phylogenetic methods in simulation. Syst. Biol. 44:17-48.
    • (1995) Syst. Biol. , vol.44 , pp. 17-48
    • Huelsenbeck, J.P.1
  • 18
    • 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. Biol. 42:247-264.
    • (1993) Syst. Biol. , vol.42 , pp. 247-264
    • Huelsenbeck, J.P.1    Hillis, D.M.2
  • 19
    • 0034849408 scopus 로고    scopus 로고
    • MrBayes: Bayesian inference of phylogeny
    • Huelsenbeck, J. P., and F. Ronquist. 2001. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17:754-755.
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 20
    • 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
  • 21
    • 0036554650 scopus 로고    scopus 로고
    • Fragmentary taxa, missing data, and ambiguity: Mistaken assumptions and conclusions
    • Kearney, M. 2002. Fragmentary taxa, missing data, and ambiguity: Mistaken assumptions and conclusions. Syst. Biol. 51:369-381.
    • (2002) Syst. Biol. , vol.51 , pp. 369-381
    • Kearney, M.1
  • 22
    • 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
  • 23
    • 0032028996 scopus 로고    scopus 로고
    • Large-scale phylogenies and measuring the effects of phylogenetic estimators
    • Kim, J. 1998. Large-scale phylogenies and measuring the effects of phylogenetic estimators. Syst. Biol. 47:43-60.
    • (1998) Syst. Biol. , vol.47 , pp. 43-60
    • Kim, J.1
  • 24
    • 0035527396 scopus 로고    scopus 로고
    • A likelihood approach to inferring phylogeny from discrete morphological characters
    • Lewis, P. O. 2001. A likelihood approach to inferring phylogeny from discrete morphological characters. Syst. Biol. 50:913-925.
    • (2001) Syst. Biol. , vol.50 , pp. 913-925
    • Lewis, P.O.1
  • 25
    • 11944252893 scopus 로고
    • Fossils, topologies, missing data, and the higher level phylogeny of eutherian mammals
    • Novacek, M. J. 1992. Fossils, topologies, missing data, and the higher level phylogeny of eutherian mammals. Syst. Biol. 41:58-73.
    • (1992) Syst. Biol. , vol.41 , pp. 58-73
    • Novacek, M.J.1
  • 27
    • 0032801377 scopus 로고    scopus 로고
    • Parsimony analysis of total evidence from extinct and extant taxa, and the cetacean-artiodactyl question
    • O'Leary M. A. 1999. Parsimony analysis of total evidence from extinct and extant taxa, and the cetacean-artiodactyl question. Cladistic 15:315-330.
    • (1999) Cladistic , vol.15 , pp. 315-330
    • O'Leary, M.A.1
  • 28
    • 0032023887 scopus 로고    scopus 로고
    • Sensitivity of phylogeny estimation to taxonomic sampling
    • Poe, S. 1998. Sensitivity of phylogeny estimation to taxonomic sampling. Syst. Biol. 47:18-31.
    • (1998) Syst. Biol. , vol.47 , pp. 18-31
    • Poe, S.1
  • 29
    • 0038487279 scopus 로고    scopus 로고
    • Evaluation of the strategy of long-branch subdivision to improve the accuracy of phylogenetic methods
    • Poe, S. 2003. Evaluation of the strategy of long-branch subdivision to improve the accuracy of phylogenetic methods. Syst. Biol. 52:423-428.
    • (2003) Syst. Biol. , vol.52 , pp. 423-428
    • Poe, S.1
  • 30
    • 0033602474 scopus 로고    scopus 로고
    • Taxon sampling revisited
    • Poe, S., and D. L. Swofford. 1999. Taxon sampling revisited. Nature 398:299-300.
    • (1999) Nature , vol.398 , pp. 299-300
    • Poe, S.1    Swofford, D.L.2
  • 31
    • 0036699885 scopus 로고    scopus 로고
    • Increased taxon sampling is advantageous for phylogenetic inference
    • Pollock, D. D., D. J. Zwickl, J. A. McGuire, and D. M. Hillis. 2002. Increased taxon sampling is advantageous for phylogenetic inference. Syst. Biol. 51:664-671.
    • (2002) Syst. Biol. , vol.51 , pp. 664-671
    • Pollock, D.D.1    Zwickl, D.J.2    McGuire, J.A.3    Hillis, D.M.4
  • 32
    • 0032225752 scopus 로고    scopus 로고
    • Taxon sampling and the accuracy of large phylogenies
    • Rannala, B., J. P. Huelsenbeck, Z. Yang, and R. Nielsen. 1998. Taxon sampling and the accuracy of large phylogenies. Syst. Biol. 47:702-710.
    • (1998) Syst. Biol. , vol.47 , pp. 702-710
    • Rannala, B.1    Huelsenbeck, J.P.2    Yang, Z.3    Nielsen, R.4
  • 33
    • 0035845536 scopus 로고    scopus 로고
    • Incomplete taxon sampling is not a problem for phylogenetic inference
    • USA
    • Rosenberg, M. S., and S. Kumar. 2001. Incomplete taxon sampling is not a problem for phylogenetic inference. Proc. Natl. Acad. Sci. USA 98:10751-10756.
    • (2001) Proc. Natl. Acad. Sci. , vol.98 , pp. 10751-10756
    • Rosenberg, M.S.1    Kumar, S.2
  • 34
    • 0037291976 scopus 로고    scopus 로고
    • Taxon sampling, bioinformatics, and phylogenomics
    • Rosenberg, M. S., and S. Kumar. 2003. Taxon sampling, bioinformatics, and phylogenomics. Syst. Biol. 52:119-124.
    • (2003) Syst. Biol. , vol.52 , pp. 119-124
    • Rosenberg, M.S.1    Kumar, S.2
  • 35
    • 0038158155 scopus 로고    scopus 로고
    • Obtaining maximal concatenated phylogenetic data sets from large sequence databases
    • Sanderson, M. J., A. C. Driskell, R. H. Ree, O. Eulenstein, and S. Langley. 2003. Obtaining maximal concatenated phylogenetic data sets from large sequence databases. Mol. Biol. Evol. 20:1036-1042.
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 1036-1042
    • Sanderson, M.J.1    Driskell, A.C.2    Ree, R.H.3    Eulenstein, O.4    Langley, S.5
  • 36
    • 0032025585 scopus 로고    scopus 로고
    • Inferring complex phylogenies using parsimony: An empirical approach using three large DNA data sets for angiosperme
    • Soltis, D. E., P. S. Soltis, M. E. Mort, M. W. Chase, V. Savolainen, S. B. Hoot, and C. M. Morton. 1998. Inferring complex phylogenies using parsimony: An empirical approach using three large DNA data sets for angiosperme. Syst. Biol. 47:32-42.
    • (1998) Syst. Biol. , vol.47 , pp. 32-42
    • Soltis, D.E.1    Soltis, P.S.2    Mort, M.E.3    Chase, M.W.4    Savolainen, V.5    Hoot, S.B.6    Morton, C.M.7
  • 39
    • 0032148650 scopus 로고    scopus 로고
    • The accuracy of methods for coding and sampling higher-level taxa for phylogenetic analysis: A simulation study
    • Wiens, J. J. 1998. The accuracy of methods for coding and sampling higher-level taxa for phylogenetic analysis: A simulation study. Syst. Biol. 47:381-397.
    • (1998) Syst. Biol. , vol.47 , pp. 381-397
    • Wiens, J.J.1
  • 40
    • 0042905752 scopus 로고    scopus 로고
    • Missing data, incomplete taxa, and phylogenetic accuracy
    • Wiens, J. J. 2003a. Missing data, incomplete taxa, and phylogenetic accuracy. Syst. Biol. 52:528-538.
    • (2003) Syst. Biol. , vol.52 , pp. 528-538
    • Wiens, J.J.1
  • 41
    • 0041592696 scopus 로고    scopus 로고
    • Incomplete taxa, incomplete characters, and phylogenetic accuracy: What is the missing data problem?
    • Wiens, J. J. 2003b. Incomplete taxa, incomplete characters, and phylogenetic accuracy: What is the missing data problem? J. Vert. Paleontol. 23:297-310.
    • (2003) J. Vert. Paleontol. , vol.23 , pp. 297-310
    • Wiens, J.J.1
  • 42
    • 0029466830 scopus 로고
    • Combining data sets with different numbers of taxa for phylogenetic analysis
    • Wiens, J. J., and T. W. Reeder. 1995. Combining data sets with different numbers of taxa for phylogenetic analysis. Syst. Biol. 44:548-558.
    • (1995) Syst. Biol. , vol.44 , pp. 548-558
    • Wiens, J.J.1    Reeder, T.W.2
  • 43
    • 0029498439 scopus 로고
    • Coping with abundant missing entries in phylogenetic inference using parsimony
    • Wilkinson, M. 1995. Coping with abundant missing entries in phylogenetic inference using parsimony. Syst. Biol. 44:501-514.
    • (1995) Syst. Biol. , vol.44 , pp. 501-514
    • Wilkinson, M.1
  • 44
    • 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
  • 45
    • 0036699481 scopus 로고    scopus 로고
    • Increased taxon sampling greatly reduces phylogenetic error
    • Zwickl, D. J., and D. M. Hillis. 2002. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 51:588-598.
    • (2002) Syst. Biol. , vol.51 , pp. 588-598
    • Zwickl, D.J.1    Hillis, D.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.