메뉴 건너뛰기




Volumn 63, Issue 5, 2014, Pages 798-811

Maximum likelihood inference of small trees in the presence of long branches

Author keywords

Analytic solutions; Long branch attraction; Maximum likelihood; Simulation

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; COMPUTER SIMULATION; MOLECULAR EVOLUTION; PHYLOGENY;

EID: 84906216105     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syu044     Document Type: Article
Times cited : (22)

References (46)
  • 1
    • 4444220955 scopus 로고    scopus 로고
    • Should we be worried about longbranch attraction in real data sets? Investigations using metazoan 18s rdna
    • Anderson F.E., Swofford D.L. 2004. Should we be worried about longbranch attraction in real data sets? Investigations using metazoan 18S rDNA. Mol. Phylogenet. and Evol. 33:440-451.
    • (2004) Mol. Phylogenet. and Evol , vol.33 , pp. 440-451
    • Anderson, F.E.1    Swofford, D.L.2
  • 2
    • 55349123605 scopus 로고    scopus 로고
    • Novel 12smtdnafindings in sloths (pilosa, folivora) and anteaters (pilosa, vermilingua) suggest a true case of long branch attraction
    • Barros M.C., Sampaio I., Schneider H. 2008. Novel 12SmtDNAfindings in sloths (Pilosa, Folivora) and anteaters (Pilosa, Vermilingua) suggest a true case of long branch attraction. Genet. Mol. Biol. 31:793-799.
    • (2008) Genet. Mol. Biol , vol.31 , pp. 793-799
    • Barros, M.C.1    Sampaio, I.2    Schneider, H.3
  • 3
    • 20444491634 scopus 로고    scopus 로고
    • A review of long-branch attraction
    • Bergsten J. 2005. A review of long-branch attraction. Cladistics 21:163-193.
    • (2005) Cladistics , vol.21 , pp. 163-193
    • Bergsten, J.1
  • 4
    • 80053182616 scopus 로고    scopus 로고
    • Along-branch attraction artifact reveals an adaptive radiation in pseudomonas
    • Bodilis J., Meilo S., Cornelius P., Vos P.D., Barray S. 2011. Along-branch attraction artifact reveals an adaptive radiation in Pseudomonas. Mol. Biol. and Evol. 28:2723-2726.
    • (2011) Mol. Biol. and Evol , vol.28 , pp. 2723-2726
    • Bodilis, J.1    Meilo, S.2    Cornelius, P.3    Vos, P.D.4    Barray, S.5
  • 5
    • 0030588055 scopus 로고    scopus 로고
    • Full reconstruction of markov models on evolutionary trees: Identifiability and consistency
    • Chang J.T. 1996. 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
  • 6
    • 12444268422 scopus 로고    scopus 로고
    • Molecular clock fork phylogenies: Closed form analytic maximum likelihood solutions
    • Chor B., Snir S. 2004. Molecular clock fork phylogenies: closed form analytic maximum likelihood solutions. Syst. Biol. 53: 963-967.
    • (2004) Syst. Biol , vol.53 , pp. 963-967
    • Chor, B.1    Snir, S.2
  • 7
    • 34547103029 scopus 로고    scopus 로고
    • Analytic solutions of maximum likelihood on forks of four taxa
    • Chor B., Snir S. 2007. Analytic solutions of maximum likelihood on forks of four taxa. Math. Biosci. 208:347-358.
    • (2007) Math. Biosci , vol.208 , pp. 347-358
    • Chor, B.1    Snir, S.2
  • 8
    • 33846781343 scopus 로고    scopus 로고
    • Analytic solutions for three taxon mlmc trees with variable rates across sites
    • Chor B., Hendy M., Penny D. 2001. Analytic solutions for three taxon MLMC trees with variable rates across sites. Discrete Appl. Math. 155:750-758.
    • (2001) Discrete Appl. Math , vol.155 , pp. 750-758
    • Chor, B.1    Hendy, M.2    Penny, D.3
  • 9
    • 33244461129 scopus 로고    scopus 로고
    • Maximum likelihood jukes-cantor triplets: Analytic solutions
    • Chor B., Hendy M., Snir S. 2006a. Maximum likelihood Jukes-Cantor triplets: analytic solutions. Mol. Biol. and Evol. 23:626-632.
    • (2006) Mol. Biol. and Evol , vol.23 , pp. 626-632
    • Chor, B.1    Hendy, M.2    Snir, S.3
  • 10
    • 33744462065 scopus 로고    scopus 로고
    • Maximumlikelihood molecular clock comb: Analytic solutions
    • Chor B., Khetan A., Snir S. 2006b. Maximumlikelihood molecular clock comb: analytic solutions. J. Comput. Biol. 13:819-837.
    • (2006) J. Comput. Biol , vol.13 , pp. 819-837
    • Chor, B.1    Khetan, A.2    Snir, S.3
  • 11
    • 77952932340 scopus 로고    scopus 로고
    • Molecular phylogeny of acariform mites (acari, arachnida): Strong conflict between phylogenetic signal and long-branch attraction artifacts
    • Dabert M., Witalinski W., Kazmierski A., Olszanowski Z., Dabert J. 2010. Molecular phylogeny of acariform mites (Acari, Arachnida): strong conflict between phylogenetic signal and long-branch attraction artifacts. Mol. Phylogenet. and Evol. 56:222-241.
    • (2010) Mol. Phylogenet. and Evol , vol.56 , pp. 222-241
    • Dabert, M.1    Witalinski, W.2    Kazmierski, A.3    Olszanowski, Z.4    Dabert, J.5
  • 12
    • 0036269480 scopus 로고    scopus 로고
    • Analyses of rna polymerase ii genes from free-living protists: Phylogeny, long branch attraction, and the eukaryotic big bang
    • Dacks J.B., Marinets A., Ford Doolittle W., Cavalier-Smith T., Logsdon J.M. 2002. Analyses of RNA Polymerase II genes from free-living protists: phylogeny, long branch attraction, and the eukaryotic big bang. Mol. Biol. and Evol. 19:830-840.
    • (2002) Mol. Biol. and Evol , vol.19 , pp. 830-840
    • Dacks, J.B.1    Marinets, A.2    Ford Doolittle, W.3    Cavalier-Smith, T.4    Logsdon, J.M.5
  • 13
    • 30744460614 scopus 로고    scopus 로고
    • Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of saccharomyces species
    • Fares M.A., Byrne K.P., Wolfe K.H. 2006. Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of Saccharomyces species. Mol. Biol. and Evol. 23:245-253.
    • (2006) Mol. Biol. and Evol , vol.23 , pp. 245-253
    • Fares, M.A.1    Byrne, K.P.2    Wolfe, K.H.3
  • 14
    • 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
  • 15
    • 0028887457 scopus 로고
    • Success of maximum likelihood phlogeny inference in the four-taxon case
    • Gaut B., Lewis P.O. 1995. Success of maximum likelihood phlogeny inference in the four-taxon case. Mol. Biol. and Evol. 12:152-162.
    • (1995) Mol. Biol. and Evol , vol.12 , pp. 152-162
    • Gaut, B.1    Lewis, P.O.2
  • 16
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximum-ikelihood phylogenies: Assessing the performance of phyml 3.0
    • Guindon S., Dufayard J., Lefort V. 2010. New algorithms and methods to estimate maximum-ikelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59:307-321.
    • (2010) Syst. Biol , vol.59 , pp. 307-321
    • Guindon, S.1    Dufayard, J.2    Lefort, V.3
  • 17
    • 0000084234 scopus 로고
    • A framework for the quantitative study of evolutionary trees
    • Hendy M.D., Penny D. 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:297.
    • (1989) Syst. Zool , vol.38 , pp. 297
    • Hendy, M.D.1    Penny, D.2
  • 18
    • 12044255023 scopus 로고
    • Success of phylogenetic methods in the four-taxon case
    • Huelsenbeck J.P., Hillis D.M. 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
    • 11944268967 scopus 로고
    • Performance of phylogenetic methods in simulation
    • Huelsenbeck J.P. 1995. Performance of phylogenetic methods in simulation. Syst. Biol. 44:17-48.
    • (1995) Syst. Biol , vol.44 , pp. 17-48
    • Huelsenbeck, J.P.1
  • 20
    • 0031084114 scopus 로고    scopus 로고
    • Is the felsenstein zone a fly trap?
    • Huelsenbeck J.P. 1997. Is the Felsenstein Zone a fly trap? Syst. Biol. 46:69-74.
    • (1997) Syst. Biol , vol.46 , pp. 69-74
    • Huelsenbeck, J.P.1
  • 21
    • 0032148641 scopus 로고    scopus 로고
    • Systematic bias in phylogenetic analysis: Is the strepsiptera problem solved?
    • Huelsenbeck J.P. 1998. Systematic bias in phylogenetic analysis: Is the Strepsiptera problem solved? Syst. Biol. 47:519-537.
    • (1998) Syst. Biol , vol.47 , pp. 519-537
    • Huelsenbeck, J.P.1
  • 22
    • 3042601821 scopus 로고    scopus 로고
    • Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in ef-1alpha phylogenies
    • Inagaki Y., Susko E., Fast N.M., Roger A.J. 2004. Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies. Mol. Biol. and Evol. 21:1340-1349.
    • (2004) Mol. Biol. and Evol , vol.21 , pp. 1340-1349
    • Inagaki, Y.1    Susko, E.2    Fast, N.M.3    Roger, A.J.4
  • 23
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • Munro, H.N., editor., New York (NY): Academic Press
    • Jukes T.H., Cantor C.R. 1969. Evolution of protein molecules. In: Munro, H.N., editor. Mammalian protein metabolism. New York (NY): Academic Press. p. 21-132.
    • (1969) Mammalian Protein Metabolism , pp. 21-132
    • Jukes, T.H.1    Cantor, C.R.2
  • 24
    • 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
  • 25
    • 0028177080 scopus 로고
    • A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates
    • Kuhner M.K., Felsenstein J. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. and Evol. 11:459-468.
    • (1994) Mol. Biol. and Evol , vol.11 , pp. 459-468
    • Kuhner, M.K.1    Felsenstein, J.2
  • 27
    • 84866512468 scopus 로고    scopus 로고
    • The impact and interplay of long and short branches on phylogenetic information content
    • Martyn I., Steel M. 2012. The impact and interplay of long and short branches on phylogenetic information content. J. Theor. Biol. 314:157-163.
    • (2012) J. Theor. Biol , vol.314 , pp. 157-163
    • Martyn, I.1    Steel, M.2
  • 29
    • 79952147429 scopus 로고    scopus 로고
    • Quantifying the impact of dependent evolution among sites in phylogenetic inference
    • Nasrallah C.A., Mathews D.H., Huelsenbeck J.P. 2011. Quantifying the impact of dependent evolution among sites in phylogenetic inference. Syst. Biol. 60:60-73.
    • (2011) Syst. Biol , vol.60 , pp. 60-73
    • Nasrallah, C.A.1    Mathews, D.H.2    Huelsenbeck, J.P.3
  • 30
    • 0035207848 scopus 로고    scopus 로고
    • Rate acceleration and long-branch attraction in a conserved gene of cryptic daphniid (crustacea) species
    • Omilian A.R., Taylor D.J. 2001. Rate acceleration and long-branch attraction in a conserved gene of cryptic daphniid (Crustacea) species. Mol. Biol. and Evol. 18:2201-2212.
    • (2001) Mol. Biol. and Evol , vol.18 , pp. 2201-2212
    • Omilian, A.R.1    Taylor, D.J.2
  • 31
    • 0034019771 scopus 로고    scopus 로고
    • Phylogeny of eukaryotes based on ribosomal RNA: Long-branch attraction and models of sequence evolution
    • Philippe H., Germot A. 2000. Phylogeny of eukaryotes based on ribosomal RNA : Long-branch attraction and models of sequence evolution. Mol. Biol. and Evol. 17:830-834.
    • (2000) Mol. Biol. and Evol , vol.17 , pp. 830-834
    • Philippe, H.1    Germot, A.2
  • 32
  • 33
    • 0035722246 scopus 로고    scopus 로고
    • Biases in maximum likelihood and parsimony: A simulation approach to a 10-taxon case
    • Pol D., Siddall M. 2001. Biases in maximum likelihood and parsimony: a simulation approach to a 10-taxon case. Cladistics 17:266-281.
    • (2001) Cladistics , vol.17 , pp. 266-281
    • Pol, D.1    Siddall, M.2
  • 34
    • 0034889910 scopus 로고    scopus 로고
    • Was the anita rooting of the angiosperm phylogeny affected by long-branch attraction? Amborella, nymphaeales, illiciales, trimeniaceae, and austrobaileya
    • Qiu Y.L., Lee J., Whitlock B., Bernasconi-Quadroni F., Dombrovska O. 2001. Was the ANITA rooting of the angiosperm phylogeny affected by long-branch attraction? Amborella, Nymphaeales, Illiciales, Trimeniaceae, and Austrobaileya. Mol. Biol. and Evol. 18: 1745-1753.
    • (2001) Mol. Biol. and Evol , vol.18 , pp. 1745-1753
    • Qiu, Y.L.1    Lee, J.2    Whitlock, B.3    Bernasconi-Quadroni, F.4    Dombrovska, O.5
  • 35
    • 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
  • 36
    • 0034069504 scopus 로고    scopus 로고
    • Error, bias, and long-branch attraction in data for two chloroplast photosystem genes in seed plants
    • Sanderson M.J., Wojciechowski M.F., Hu J.M., Khan T.S., Brady S.G. 2000. Error, bias, and long-branch attraction in data for two chloroplast photosystem genes in seed plants. Mol. Biol. and Evol. 17:782-797.
    • (2000) Mol. Biol. and Evol , vol.17 , pp. 782-797
    • Sanderson, M.J.1    Wojciechowski, M.F.2    Hu, J.M.3    Khan, T.S.4    Brady, S.G.5
  • 37
    • 4644356723 scopus 로고    scopus 로고
    • Inconsistency of maximum parsimony revisited
    • Schulmeister S. 2004. Inconsistency of maximum parsimony revisited. Syst. Biol. 53:521-528.
    • (2004) Syst. Biol , vol.53 , pp. 521-528
    • Schulmeister, S.1
  • 38
    • 10644253746 scopus 로고    scopus 로고
    • Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?
    • Stefanović S., Rice D.W., Palmer J.D. 2004. Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots? BMC Evol. Biol. 4:35.
    • (2004) BMC Evol. Biol , vol.4 , pp. 35
    • Stefanović, S.1    Rice, D.W.2    Palmer, J.D.3
  • 39
    • 0032871269 scopus 로고    scopus 로고
    • Long-branch attraction and therdnamodel of early eukaryotic evolution
    • Stiller J.W., Hall B.D. 1999. Long-branch attraction and therDNAmodel of early eukaryotic evolution. Mol. Biol. and Evol. 16:1270-1279.
    • (1999) Mol. Biol. and Evol , vol.16 , pp. 1270-1279
    • Stiller, J.W.1    Hall, B.D.2
  • 40
    • 0002671410 scopus 로고
    • Some probabilistic and statistical problems in the analysis of dna sequences
    • Tavaré S. 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. Lect. Math. Life Sci. 17:57-86.
    • (1986) Lect. Math. Life Sci , vol.17 , pp. 57-86
    • Tavaré, S.1
  • 41
    • 0034350374 scopus 로고    scopus 로고
    • War of the iguanas: Conflicting molecular and morphological phylogenies and long-branch attraction in iguanid lizards
    • Wiens J.J., Hollingsworth B.D. 2000. War of the Iguanas: conflicting molecular and morphological phylogenies and long-branch attraction in iguanid lizards. Syst. Biol. 49:143-159.
    • (2000) Syst. Biol , vol.49 , pp. 143-159
    • Wiens, J.J.1    Hollingsworth, B.D.2
  • 43
    • 0034700877 scopus 로고    scopus 로고
    • Complexity of the simplest phylogenetic estimation problem
    • Yang Z. 2000. Complexity of the simplest phylogenetic estimation problem. Proc. R. Soc. Lond. B 267:109-116.
    • (2000) Proc. R. Soc. Lond. B , vol.267 , pp. 109-116
    • Yang, Z.1
  • 45
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. and Evol. 24:1586-1591.
    • (2007) Mol. Biol. and Evol , vol.24 , pp. 1586-1591
    • Yang, Z.1
  • 46
    • 0026443498 scopus 로고
    • Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock
    • Zharkikh A., Li W.H. 1992. Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock. Mol. Biol. and Evol. 9:1119-1147.
    • (1992) Mol. Biol. and Evol , vol.9 , pp. 1119-1147
    • Zharkikh, A.1    Li, W.H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.