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Volumn 78, Issue 1, 2014, Pages 334-348

Dubious resolution and support from published sparse supermatrices: The importance of thorough tree searches

Author keywords

Maximum likelihood; Parsimony; Rapid bootstrap; RAxML; SH like aLRT; Tree hybridization

Indexed keywords

DNA SEQUENCE; PHYLOGENY; STATISTICAL MODEL;

EID: 84904622865     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2014.06.002     Document Type: Article
Times cited : (25)

References (96)
  • 2
    • 33745256005 scopus 로고    scopus 로고
    • Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative
    • Anisimova M., Gascuel O. Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst. Biol. 2006, 55:539-552.
    • (2006) Syst. Biol. , vol.55 , pp. 539-552
    • Anisimova, M.1    Gascuel, O.2
  • 3
    • 80053107842 scopus 로고    scopus 로고
    • Inferring the tree of life: chopping a phylogenomic problem down to size?
    • Bininda-Emonds O.R.P. Inferring the tree of life: chopping a phylogenomic problem down to size?. BMC Biol. 2011, 9:59.
    • (2011) BMC Biol. , vol.9 , pp. 59
    • Bininda-Emonds, O.R.P.1
  • 4
    • 84986251481 scopus 로고    scopus 로고
    • Taxon sampling versus computational complexity and their impact on obtaining the tree of life
    • CRC Press, Boca Raton, T.R. Hodkinson, J.A.N. Parnell (Eds.)
    • Bininda-Emonds O.R.P., Stamatakis A. Taxon sampling versus computational complexity and their impact on obtaining the tree of life. Reconstructing The Tree of life: Taxonomy and Systematics of Species Rich Taxa 2007, 77-95. CRC Press, Boca Raton. T.R. Hodkinson, J.A.N. Parnell (Eds.).
    • (2007) Reconstructing The Tree of life: Taxonomy and Systematics of Species Rich Taxa , pp. 77-95
    • Bininda-Emonds, O.R.P.1    Stamatakis, A.2
  • 5
    • 0000367652 scopus 로고
    • The limits of amino acid sequence data in angiosperm phylogenetic reconstruction
    • Bremer K. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 1988, 42:795-803.
    • (1988) Evolution , vol.42 , pp. 795-803
    • Bremer, K.1
  • 6
    • 33751012343 scopus 로고    scopus 로고
    • The limits of conventional cladistic analysis
    • Oxford University Press, Oxford, V.A. Albert (Ed.)
    • Davis J.I., Nixon K.C., Little D.P. The limits of conventional cladistic analysis. Parsimony, Phylogeny, and Genomics 2005, 119-147. Oxford University Press, Oxford. V.A. Albert (Ed.).
    • (2005) Parsimony, Phylogeny, and Genomics , pp. 119-147
    • Davis, J.I.1    Nixon, K.C.2    Little, D.P.3
  • 7
    • 67449167484 scopus 로고    scopus 로고
    • Properties of consensus methods for inferring species trees from gene trees
    • Degnan J.H., DeGiorgio M., Bryant D., Rosenberg N.A. Properties of consensus methods for inferring species trees from gene trees. Syst. Biol. 2009, 58:35-54.
    • (2009) Syst. Biol. , vol.58 , pp. 35-54
    • Degnan, J.H.1    DeGiorgio, M.2    Bryant, D.3    Rosenberg, N.A.4
  • 9
    • 0000989175 scopus 로고
    • Gene trees and species trees: molecular systematics as one-character taxonomy
    • Doyle J.J. Gene trees and species trees: molecular systematics as one-character taxonomy. Syst. Bot. 1992, 17:144-163.
    • (1992) Syst. Bot. , vol.17 , pp. 144-163
    • Doyle, J.J.1
  • 10
    • 74949137624 scopus 로고    scopus 로고
    • Patterns of macroevolution among primates inferred from a supermatrix of mitochondrial and nuclear DNA
    • Fabre P.-H., Rodrigues A., Douzery E.J.P. Patterns of macroevolution among primates inferred from a supermatrix of mitochondrial and nuclear DNA. Mol. Phylogenet. Evol. 2009, 53:808-825.
    • (2009) Mol. Phylogenet. Evol. , vol.53 , pp. 808-825
    • Fabre, P.-H.1    Rodrigues, A.2    Douzery, E.J.P.3
  • 11
    • 84963071608 scopus 로고
    • On comparing the shapes of taxonomic trees
    • Farris J.S. On comparing the shapes of taxonomic trees. Syst. Zool. 1973, 22:50-54.
    • (1973) Syst. Zool. , vol.22 , pp. 50-54
    • Farris, J.S.1
  • 13
    • 84959848780 scopus 로고
    • Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters
    • Felsenstein J. Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Syst. Zool. 1973, 22:240-249.
    • (1973) Syst. Zool. , vol.22 , pp. 240-249
    • Felsenstein, J.1
  • 14
    • 84959792503 scopus 로고
    • The number of evolutionary trees
    • Felsenstein J. The number of evolutionary trees. Syst. Zool. 1978, 27:27-33.
    • (1978) Syst. Zool. , vol.27 , pp. 27-33
    • Felsenstein, J.1
  • 15
    • 84959798530 scopus 로고
    • Cases in which parsimony or compatibility methods will be positively misleading
    • Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 1978, 27:401-410.
    • (1978) Syst. Zool. , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 16
    • 84959747425 scopus 로고
    • Toward defining the course of evolution: minimum change for a specific tree topology
    • Fitch W.M. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 1971, 20:406-416.
    • (1971) Syst. Zool. , vol.20 , pp. 406-416
    • Fitch, W.M.1
  • 17
    • 78349298734 scopus 로고    scopus 로고
    • Branch support via resampling: an empirical study
    • Freudenstein J.V., Davis J.I. Branch support via resampling: an empirical study. Cladistics 2010, 26:643-656.
    • (2010) Cladistics , vol.26 , pp. 643-656
    • Freudenstein, J.V.1    Davis, J.I.2
  • 19
    • 84875547630 scopus 로고    scopus 로고
    • Concatenation versus coalescence versus "concatalescence"
    • Gatesy J., Springer M.S. Concatenation versus coalescence versus "concatalescence". Proc. Natl. Acad. Sci. USA 2013, 110:E1179.
    • (2013) Proc. Natl. Acad. Sci. USA , vol.110
    • Gatesy, J.1    Springer, M.S.2
  • 21
    • 0033499153 scopus 로고    scopus 로고
    • Analyzing large data sets in reasonable times: solutions for composite optima
    • Goloboff P.A. Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics 1999, 15:415-428.
    • (1999) Cladistics , vol.15 , pp. 415-428
    • Goloboff, P.A.1
  • 22
    • 69949087760 scopus 로고    scopus 로고
    • Tratamiento de la ambigüedad en grandes matrices de datos
    • Goloboff P.A. Tratamiento de la ambigüedad en grandes matrices de datos. Darwiniana 2007, 45:S10-S11.
    • (2007) Darwiniana , vol.45
    • Goloboff, P.A.1
  • 23
    • 0035012476 scopus 로고    scopus 로고
    • Methods for quick consensus estimation
    • Goloboff P.A., Farris J.S. Methods for quick consensus estimation. Cladistics 2001, 17:S26-S34.
    • (2001) Cladistics , vol.17
    • Goloboff, P.A.1    Farris, J.S.2
  • 24
    • 34548554071 scopus 로고    scopus 로고
    • On divide-and-conquer strategies for parsimony analysis of large data sets: Rec-I-DCM3 versus TNT
    • Goloboff P.A., Pol D. On divide-and-conquer strategies for parsimony analysis of large data sets: Rec-I-DCM3 versus TNT. Syst. Biol. 2007, 56:485-495.
    • (2007) Syst. Biol. , vol.56 , pp. 485-495
    • Goloboff, P.A.1    Pol, D.2
  • 26
    • 45749124657 scopus 로고    scopus 로고
    • TNT, a free program for phylogenetic analysis
    • Goloboff P.A., Farris J.S., Nixon K.C. TNT, a free program for phylogenetic analysis. Cladistics 2008, 24:774-786.
    • (2008) Cladistics , vol.24 , pp. 774-786
    • Goloboff, P.A.1    Farris, J.S.2    Nixon, K.C.3
  • 28
    • 0020400261 scopus 로고
    • New perspectives in the molecular biological analysis of mammalian phylogeny
    • Goodman M., Olson C.B., Beeber J.E., Czelusniak J. New perspectives in the molecular biological analysis of mammalian phylogeny. Acta Zool. Fenn. 1985, 169:19-35.
    • (1985) Acta Zool. Fenn. , vol.169 , pp. 19-35
    • Goodman, M.1    Olson, C.B.2    Beeber, J.E.3    Czelusniak, J.4
  • 29
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
    • Guindon S., Dufayard J.-F., Lefort V., Anisimova M., Hordijk W., Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 2010, 59:307-321.
    • (2010) Syst. Biol. , vol.59 , pp. 307-321
    • Guindon, S.1    Dufayard, J.-F.2    Lefort, V.3    Anisimova, M.4    Hordijk, W.5    Gascuel, O.6
  • 30
    • 84879819415 scopus 로고    scopus 로고
    • The bee tree of life: a supermatrix approach to apoid phylogeny and biogeography
    • Hedtke S.M., Patiny S., Danforth B.N. The bee tree of life: a supermatrix approach to apoid phylogeny and biogeography. BMC Evol. Biol. 2013, 13:138.
    • (2013) BMC Evol. Biol. , vol.13 , pp. 138
    • Hedtke, S.M.1    Patiny, S.2    Danforth, B.N.3
  • 31
    • 84873597223 scopus 로고    scopus 로고
    • Using supermatrices for phylogenetic inquiry: an example using the sedges
    • Hinchliff C.E., Roalson E.H. Using supermatrices for phylogenetic inquiry: an example using the sedges. Syst. Biol. 2013, 62:205-219.
    • (2013) Syst. Biol. , vol.62 , pp. 205-219
    • Hinchliff, C.E.1    Roalson, E.H.2
  • 32
    • 0036806280 scopus 로고    scopus 로고
    • Potential applications and pitfalls of Bayesian inference of phylogeny
    • Huelsenbeck J.P., Larget B., Miller R.E., Ronquist F. Potential applications and pitfalls of Bayesian inference of phylogeny. Syst. Biol. 2002, 51:673-688.
    • (2002) Syst. Biol. , vol.51 , pp. 673-688
    • Huelsenbeck, J.P.1    Larget, B.2    Miller, R.E.3    Ronquist, F.4
  • 33
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • Academic Press, New York
    • Jukes T.H., Cantor C.R. Evolution of protein molecules. Mammalian Protein Metabolism 1969, vol. 3:21-132. Academic Press, New York.
    • (1969) Mammalian Protein Metabolism , vol.3 , pp. 21-132
    • Jukes, T.H.1    Cantor, C.R.2
  • 35
    • 84876577912 scopus 로고    scopus 로고
    • Legume phylogeny and classification in the 21st century: progress, prospects and lessons for other species-rich clades
    • Legume Phylogeny Working Group
    • Legume Phylogeny Working Group Legume phylogeny and classification in the 21st century: progress, prospects and lessons for other species-rich clades. Taxon 2013, 62:217-248.
    • (2013) Taxon , vol.62 , pp. 217-248
  • 36
    • 67449163699 scopus 로고    scopus 로고
    • The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference
    • Lemmon A.R., Brown J.M., Stanger-Hall K., Lemmon E.M. The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Syst. Biol. 2009, 58:130-145.
    • (2009) Syst. Biol. , vol.58 , pp. 130-145
    • Lemmon, A.R.1    Brown, J.M.2    Stanger-Hall, K.3    Lemmon, E.M.4
  • 37
    • 77957686501 scopus 로고    scopus 로고
    • A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
    • Liu L., Yu L., Edwards S.V. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol. Biol. 2010, 10:302.
    • (2010) BMC Evol. Biol. , vol.10 , pp. 302
    • Liu, L.1    Yu, L.2    Edwards, S.V.3
  • 39
    • 84960569058 scopus 로고
    • The discovery and importance of multiple islands of most-parsimonious trees
    • Maddison D.R. The discovery and importance of multiple islands of most-parsimonious trees. Syst. Zool. 1991, 40:315-328.
    • (1991) Syst. Zool. , vol.40 , pp. 315-328
    • Maddison, D.R.1
  • 40
    • 84904638466 scopus 로고    scopus 로고
    • MacClade: Analysis of Phylogeny and Character Evolution, Version 4.03. Sunderland, Sinauer.
    • Maddison, D.R., Maddison, W.P., 2001. MacClade: Analysis of Phylogeny and Character Evolution, Version 4.03. Sunderland, Sinauer.
    • (2001)
    • Maddison, D.R.1    Maddison, W.P.2
  • 41
    • 84904611883 scopus 로고    scopus 로고
    • Mesquite: A Modular System for Evolutionary Analysis. Published by the authors,
    • Maddison, W.P., Maddison, D.R., 2013. Mesquite: A Modular System for Evolutionary Analysis. Published by the authors, http://www.mesquiteproject.org/mesquite/mesquite.html.
    • (2013)
    • Maddison, W.P.1    Maddison, D.R.2
  • 43
    • 0037767303 scopus 로고    scopus 로고
    • The misleading effects of composite taxa in supermatrices
    • Malia M.J., Lipscomb D.L., Allard M.W. The misleading effects of composite taxa in supermatrices. Mol. Phylogenet. Evol. 2003, 27:522-527.
    • (2003) Mol. Phylogenet. Evol. , vol.27 , pp. 522-527
    • Malia, M.J.1    Lipscomb, D.L.2    Allard, M.W.3
  • 45
    • 72049096137 scopus 로고    scopus 로고
    • Cryptic failure of partitioned Bayesian phylogenetic analyses: lost in the land of long trees
    • Marshall D.C. Cryptic failure of partitioned Bayesian phylogenetic analyses: lost in the land of long trees. Syst. Biol. 2010, 59:108-117.
    • (2010) Syst. Biol. , vol.59 , pp. 108-117
    • Marshall, D.C.1
  • 46
    • 34547803149 scopus 로고    scopus 로고
    • Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes
    • McMahon M.M., Sanderson M.J. Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes. Syst. Biol. 2006, 55:818-836.
    • (2006) Syst. Biol. , vol.55 , pp. 818-836
    • McMahon, M.M.1    Sanderson, M.J.2
  • 47
    • 39549109362 scopus 로고    scopus 로고
    • Increasing the efficiency of searches for the maximum likelihood tree in a phylogenetic analysis of up to 150 nucleotide sequences
    • Morrison D.A. Increasing the efficiency of searches for the maximum likelihood tree in a phylogenetic analysis of up to 150 nucleotide sequences. Syst. Biol. 2007, 56:988-1010.
    • (2007) Syst. Biol. , vol.56 , pp. 988-1010
    • Morrison, D.A.1
  • 48
    • 84904636558 scopus 로고    scopus 로고
    • Evolutionary genomics: statistical and computational methods. Volumes 1 and 2
    • Morrison D.A. Evolutionary genomics: statistical and computational methods. Volumes 1 and 2. Syst. Biol. 2013, 62:348-350.
    • (2013) Syst. Biol. , vol.62 , pp. 348-350
    • Morrison, D.A.1
  • 49
    • 0030934592 scopus 로고    scopus 로고
    • Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of Apicomplexa
    • Morrison D.A., Ellis J.T. Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of Apicomplexa. Mol. Biol. Evol. 1997, 14:428-441.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 428-441
    • Morrison, D.A.1    Ellis, J.T.2
  • 50
    • 27744567179 scopus 로고    scopus 로고
    • The efficiency of different search strategies in estimating parsimony jackknife, bootstrap, and Bremer support
    • Müller K. The efficiency of different search strategies in estimating parsimony jackknife, bootstrap, and Bremer support. BMC Evol. Biol. 2005, 5:58.
    • (2005) BMC Evol. Biol. , vol.5 , pp. 58
    • Müller, K.1
  • 51
    • 0033504552 scopus 로고    scopus 로고
    • The parsimony ratchet, a new method for rapid parsimony analysis
    • Nixon K.C. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 1999, 15:407-414.
    • (1999) Cladistics , vol.15 , pp. 407-414
    • Nixon, K.C.1
  • 52
    • 0030378088 scopus 로고    scopus 로고
    • On consensus, collapsibility, and clade concordance
    • Nixon K.C., Carpenter J.M. On consensus, collapsibility, and clade concordance. Cladistics 1996, 12:305-321.
    • (1996) Cladistics , vol.12 , pp. 305-321
    • Nixon, K.C.1    Carpenter, J.M.2
  • 53
    • 0002272008 scopus 로고
    • Extinction and the origin of species
    • Columbia University Press, New York, Q.D. Wheeler, M. Novacek (Eds.)
    • Nixon K.C., Wheeler Q.D. Extinction and the origin of species. Extinction and Phylogeny 1991, 119-143. Columbia University Press, New York. Q.D. Wheeler, M. Novacek (Eds.).
    • (1991) Extinction and Phylogeny , pp. 119-143
    • Nixon, K.C.1    Wheeler, Q.D.2
  • 54
    • 84857422378 scopus 로고    scopus 로고
    • Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates
    • Nyakatura K., Bininda-Emonds O.R.P. Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates. BMC Biol. 2012, 10:12.
    • (2012) BMC Biol. , vol.10 , pp. 12
    • Nyakatura, K.1    Bininda-Emonds, O.R.P.2
  • 55
    • 0026495826 scopus 로고
    • Progress with methods for constructing evolutionary trees
    • Penny D., Hendy M.D., Steel M.A. Progress with methods for constructing evolutionary trees. Trends Ecol. Evol. 1992, 7:73-79.
    • (1992) Trends Ecol. Evol. , vol.7 , pp. 73-79
    • Penny, D.1    Hendy, M.D.2    Steel, M.A.3
  • 56
    • 80051801316 scopus 로고    scopus 로고
    • The taming of an impossible child: a standardized all-in approach to the phylogeny of Hymenoptera using public database sequences
    • Peters R.S., Meyer B., Krogmann L., Borner J., Meusemann K., Schutte K., Niehuis O., Misof B. The taming of an impossible child: a standardized all-in approach to the phylogeny of Hymenoptera using public database sequences. BMC Biol. 2011, 9:55.
    • (2011) BMC Biol. , vol.9 , pp. 55
    • Peters, R.S.1    Meyer, B.2    Krogmann, L.3    Borner, J.4    Meusemann, K.5    Schutte, K.6    Niehuis, O.7    Misof, B.8
  • 57
    • 80052717965 scopus 로고    scopus 로고
    • A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians
    • Pyron R.A., Wiens J.J. A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians. Mol. Phylogenet. Evol. 2011, 61:543-583.
    • (2011) Mol. Phylogenet. Evol. , vol.61 , pp. 543-583
    • Pyron, R.A.1    Wiens, J.J.2
  • 58
    • 79951578515 scopus 로고    scopus 로고
    • The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees
    • Pyron R.A., Burbrink F.T., Colli G.R., Montes de Oca A.N., Vitt L.J., Kurynski C.A., Wiens J.J. The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees. Mol. Phylogenet. Evol. 2011, 58:329-342.
    • (2011) Mol. Phylogenet. Evol. , vol.58 , pp. 329-342
    • Pyron, R.A.1    Burbrink, F.T.2    Colli, G.R.3    Montes de Oca, A.N.4    Vitt, L.J.5    Kurynski, C.A.6    Wiens, J.J.7
  • 59
    • 79955724832 scopus 로고    scopus 로고
    • Do model-based phylogenetic analyses perform better than parsimony? A test with empirical data
    • Rindal E., Brower A.V.Z. Do model-based phylogenetic analyses perform better than parsimony? A test with empirical data. Cladistics 2011, 27:331-334.
    • (2011) Cladistics , vol.27 , pp. 331-334
    • Rindal, E.1    Brower, A.V.Z.2
  • 61
    • 84871842306 scopus 로고    scopus 로고
    • Impact of missing data on phylogenies inferred from empirical phylogenomic data sets
    • Roure B., Baurain D., Philippe H. Impact of missing data on phylogenies inferred from empirical phylogenomic data sets. Mol. Biol. Evol. 2013, 30:197-214.
    • (2013) Mol. Biol. Evol. , vol.30 , pp. 197-214
    • Roure, B.1    Baurain, D.2    Philippe, H.3
  • 62
    • 0037314098 scopus 로고    scopus 로고
    • R8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
    • Sanderson M.J. R8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 2003, 19:301-302.
    • (2003) Bioinformatics , vol.19 , pp. 301-302
    • Sanderson, M.J.1
  • 63
    • 11944255719 scopus 로고
    • Reconstruction of organismal and gene phylogenies from data on multigene families: concerted evolution, homoplasy, and confidence
    • Sanderson M.J., Doyle J.J. Reconstruction of organismal and gene phylogenies from data on multigene families: concerted evolution, homoplasy, and confidence. Syst. Biol. 1992, 41:4-17.
    • (1992) Syst. Biol. , vol.41 , pp. 4-17
    • Sanderson, M.J.1    Doyle, J.J.2
  • 64
    • 0034351397 scopus 로고    scopus 로고
    • Parametric phylogenetics?
    • Sanderson M.J., Kim J. Parametric phylogenetics?. Syst. Biol. 2000, 49:817-829.
    • (2000) Syst. Biol. , vol.49 , pp. 817-829
    • Sanderson, M.J.1    Kim, J.2
  • 65
    • 0032030505 scopus 로고    scopus 로고
    • Phylogenetic supertrees: assembling the trees of life
    • Sanderson M.J., Purvis A., Henze C. Phylogenetic supertrees: assembling the trees of life. Trends Ecol. Evol. 1998, 13:105-109.
    • (1998) Trends Ecol. Evol. , vol.13 , pp. 105-109
    • Sanderson, M.J.1    Purvis, A.2    Henze, C.3
  • 66
    • 77952490857 scopus 로고    scopus 로고
    • Phylogenomics with incomplete taxon coverage: the limits of inference
    • Sanderson M.J., McMahon M.J., Steel M. Phylogenomics with incomplete taxon coverage: the limits of inference. BMC Evol. Biol. 2010, 10:155.
    • (2010) BMC Evol. Biol. , vol.10 , pp. 155
    • Sanderson, M.J.1    McMahon, M.J.2    Steel, M.3
  • 67
    • 79960670940 scopus 로고    scopus 로고
    • Terraces in phylogenetic tree space
    • Sanderson M.J., McMahon M.M., Steel M. Terraces in phylogenetic tree space. Science 2011, 333:448-450.
    • (2011) Science , vol.333 , pp. 448-450
    • Sanderson, M.J.1    McMahon, M.M.2    Steel, M.3
  • 68
    • 0000459582 scopus 로고
    • Locating the vertices of a steiner tree in an arbitrary metric space
    • Sankoff D., Rousseau P. Locating the vertices of a steiner tree in an arbitrary metric space. Math. Program. 1975, 9:240-246.
    • (1975) Math. Program. , vol.9 , pp. 240-246
    • Sankoff, D.1    Rousseau, P.2
  • 69
    • 0002657605 scopus 로고
    • Analysis of taxonomic congruence among morphological, ecological, and biogeographic data sets for the Leptopodomorpha (Hemiptera)
    • Schuh R.T., Polhemus J.T. Analysis of taxonomic congruence among morphological, ecological, and biogeographic data sets for the Leptopodomorpha (Hemiptera). Syst. Zool. 1980, 29:1-26.
    • (1980) Syst. Zool. , vol.29 , pp. 1-26
    • Schuh, R.T.1    Polhemus, J.T.2
  • 70
    • 0032766857 scopus 로고    scopus 로고
    • Multiple comparisons of log-likelihoods with applications to phylogenetic inference
    • Shimodaira H., Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 1999, 16:1114-1116.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1114-1116
    • Shimodaira, H.1    Hasegawa, M.2
  • 71
    • 77954501352 scopus 로고    scopus 로고
    • Unringing a bell: metazoan phylogenomics and the partition bootstrap
    • Siddall M.E. Unringing a bell: metazoan phylogenomics and the partition bootstrap. Cladistics 2010, 26:444-452.
    • (2010) Cladistics , vol.26 , pp. 444-452
    • Siddall, M.E.1
  • 72
    • 83655167077 scopus 로고    scopus 로고
    • Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data
    • Simmons M.P. Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data. Mol. Phylogenet. Evol. 2012, 62:472-484.
    • (2012) Mol. Phylogenet. Evol. , vol.62 , pp. 472-484
    • Simmons, M.P.1
  • 73
    • 84858080561 scopus 로고    scopus 로고
    • Misleading results of likelihood-based phylogenetic analyses in the presence of missing data
    • Simmons M.P. Misleading results of likelihood-based phylogenetic analyses in the presence of missing data. Cladistics 2012, 28:208-222.
    • (2012) Cladistics , vol.28 , pp. 208-222
    • Simmons, M.P.1
  • 74
    • 84894609144 scopus 로고    scopus 로고
    • Limitations of locally sampled characters in phylogenetic analyses of sparse supermatrices
    • Simmons M.P. Limitations of locally sampled characters in phylogenetic analyses of sparse supermatrices. Mol. Phylogenet. Evol. 2014, 74:1-14.
    • (2014) Mol. Phylogenet. Evol. , vol.74 , pp. 1-14
    • Simmons, M.P.1
  • 75
    • 79960573402 scopus 로고    scopus 로고
    • Spurious 99% bootstrap and jackknife support for unsupported clades
    • Simmons M.P., Freudenstein J.V. Spurious 99% bootstrap and jackknife support for unsupported clades. Mol. Phylogenet. Evol. 2011, 61:177-191.
    • (2011) Mol. Phylogenet. Evol. , vol.61 , pp. 177-191
    • Simmons, M.P.1    Freudenstein, J.V.2
  • 76
    • 84880157756 scopus 로고    scopus 로고
    • An artifact caused by undersampling optimal trees in supermatrix analyses of locally sampled characters
    • Simmons M.P., Goloboff P.A. An artifact caused by undersampling optimal trees in supermatrix analyses of locally sampled characters. Mol. Phylogenet. Evol. 2013, 69:265-275.
    • (2013) Mol. Phylogenet. Evol. , vol.69 , pp. 265-275
    • Simmons, M.P.1    Goloboff, P.A.2
  • 77
    • 84875054472 scopus 로고    scopus 로고
    • Quantification and relative severity of inflated branch-support values generated by alternative methods: an empirical example
    • Simmons M.P., Norton A.P. Quantification and relative severity of inflated branch-support values generated by alternative methods: an empirical example. Mol. Phylogenet. Evol. 2013, 67:277-296.
    • (2013) Mol. Phylogenet. Evol. , vol.67 , pp. 277-296
    • Simmons, M.P.1    Norton, A.P.2
  • 78
    • 84896270356 scopus 로고    scopus 로고
    • Divergent maximum-likelihood-branch-support values for polytomies
    • Simmons M.P., Norton A.P. Divergent maximum-likelihood-branch-support values for polytomies. Mol. Phylogenet. Evol. 2014, 73:87-96.
    • (2014) Mol. Phylogenet. Evol. , vol.73 , pp. 87-96
    • Simmons, M.P.1    Norton, A.P.2
  • 79
    • 84901451257 scopus 로고    scopus 로고
    • Disparate parametric branch-support values from ambiguous characters
    • Simmons M.P., Randle C.P. Disparate parametric branch-support values from ambiguous characters. Mol. Phylogenet. Evol. 2014, 78:66-86.
    • (2014) Mol. Phylogenet. Evol. , vol.78 , pp. 66-86
    • Simmons, M.P.1    Randle, C.P.2
  • 80
    • 33745034045 scopus 로고    scopus 로고
    • Quantification of the success of phylogenetic inference in simulations
    • Simmons M.P., Webb C.T. Quantification of the success of phylogenetic inference in simulations. Cladistics 2006, 22:249-255.
    • (2006) Cladistics , vol.22 , pp. 249-255
    • Simmons, M.P.1    Webb, C.T.2
  • 81
    • 33847240958 scopus 로고    scopus 로고
    • A 567-taxon data set for angiosperms: the challenges posed by Bayesian analyses of large data sets
    • Soltis D.E., Gitzendanner M.A., Soltis P.S. A 567-taxon data set for angiosperms: the challenges posed by Bayesian analyses of large data sets. Int. J. Plant Sci. 2007, 168:137-157.
    • (2007) Int. J. Plant Sci. , vol.168 , pp. 137-157
    • Soltis, D.E.1    Gitzendanner, M.A.2    Soltis, P.S.3
  • 84
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 85
    • 84904664497 scopus 로고    scopus 로고
    • The RAxML v8.0.X manual. (downloaded 04.03.14).
    • Stamatakis, A., 2014. The RAxML v8.0.X manual. (downloaded 04.03.14). http://www.sco.h-its.org/exelixis/resource/download/NewManual.pdf.
    • (2014)
    • Stamatakis, A.1
  • 86
    • 50249100595 scopus 로고    scopus 로고
    • A rapid bootstrap algorithm for the RAxML web servers
    • Stamatakis A., Hoover P., Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst. Biol. 2008, 57:758-771.
    • (2008) Syst. Biol. , vol.57 , pp. 758-771
    • Stamatakis, A.1    Hoover, P.2    Rougemont, J.3
  • 87
    • 75149150388 scopus 로고    scopus 로고
    • TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses
    • Stöver B.C., Müller K.F. TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics 2010, 11:7.
    • (2010) BMC Bioinformatics , vol.11 , pp. 7
    • Stöver, B.C.1    Müller, K.F.2
  • 88
    • 77954202497 scopus 로고    scopus 로고
    • DendroPy: a python library for phylogenetic computing
    • Sukumaran J., Holder M.T. DendroPy: a python library for phylogenetic computing. Bioinformatics 2010, 26:1569-1571.
    • (2010) Bioinformatics , vol.26 , pp. 1569-1571
    • Sukumaran, J.1    Holder, M.T.2
  • 89
    • 62649109946 scopus 로고    scopus 로고
    • Incomparability of results between phylogenetic search programs. In: Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology (BIOCOMP'08)
    • Sundberg, K., Carroll, H., Snell, Q., Clement, M., 2008. Incomparability of results between phylogenetic search programs. In: Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology (BIOCOMP'08), pp. 81-84.
    • (2008) , pp. 81-84
    • Sundberg, K.1    Carroll, H.2    Snell, Q.3    Clement, M.4
  • 91
    • 80052752932 scopus 로고    scopus 로고
    • Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation
    • Townsend T.M., Mulcahy D.G., Noonan B.P., Sites J.W., Kuczynski C.A., Wiens J.J., Reeder T.W. Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation. Mol. Phylogenet. Evol. 2011, 61:363-380.
    • (2011) Mol. Phylogenet. Evol. , vol.61 , pp. 363-380
    • Townsend, T.M.1    Mulcahy, D.G.2    Noonan, B.P.3    Sites, J.W.4    Kuczynski, C.A.5    Wiens, J.J.6    Reeder, T.W.7
  • 92
    • 77954513314 scopus 로고    scopus 로고
    • A supermatrix-based molecular phylogeny of the family Drosophilidae
    • van der Linde K., Houle D., Spicer G.S., Steppan S.J. A supermatrix-based molecular phylogeny of the family Drosophilidae. Genet. Res. 2010, 92:25-38.
    • (2010) Genet. Res. , vol.92 , pp. 25-38
    • van der Linde, K.1    Houle, D.2    Spicer, G.S.3    Steppan, S.J.4
  • 93
    • 80052006478 scopus 로고    scopus 로고
    • Missing data in phylogenetic analysis: reconciling results from simulations and empirical data
    • Wiens J.J., Morrill M.C. Missing data in phylogenetic analysis: reconciling results from simulations and empirical data. Syst. Biol. 2011, 60:719-731.
    • (2011) Syst. Biol. , vol.60 , pp. 719-731
    • Wiens, J.J.1    Morrill, M.C.2
  • 94
    • 70350618257 scopus 로고    scopus 로고
    • Molecular phylogenetics: mathematical framework and unsolved problems
    • Springer, New York City, U. Bastolla, M. Porto, H.E. Roman, M. Vendruscolo (Eds.)
    • Xia X. Molecular phylogenetics: mathematical framework and unsolved problems. Structural Approaches to Sequence Evolution 2006, 171-191. Springer, New York City. U. Bastolla, M. Porto, H.E. Roman, M. Vendruscolo (Eds.).
    • (2006) Structural Approaches to Sequence Evolution , pp. 171-191
    • Xia, X.1
  • 95
    • 0030749810 scopus 로고    scopus 로고
    • Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo method
    • Yang Z., Rannala B. Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo method. Mol. Biol. Evol. 1997, 14:717-724.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 717-724
    • Yang, Z.1    Rannala, B.2
  • 96
    • 84904660143 scopus 로고    scopus 로고
    • Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets under the Maximum Likelihood Criterion. Ph.D. Dissertation, The University of Texas at Austin.
    • Zwickl, D.J., 2006. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets under the Maximum Likelihood Criterion. Ph.D. Dissertation, The University of Texas at Austin.
    • (2006)
    • Zwickl, D.J.1


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