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Volumn 45, Issue 1, 2007, Pages 81-88

The effect of branch lengths on phylogeny: An empirical study using highly conserved orthologs from mammalian genomes

Author keywords

Long branch attraction; Mammalian phylogeny; Opposite branch attraction; Phylogenetic methods

Indexed keywords

ANIMAL; ARTICLE; CHICKEN; COMPARATIVE STUDY; DOG; GENETIC VARIABILITY; GENETICS; GENOME; HUMAN; MAMMAL; MOLECULAR EVOLUTION; MOUSE; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE HOMOLOGY;

EID: 34548543988     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2007.04.022     Document Type: Article
Times cited : (7)

References (37)
  • 2
    • 4444220955 scopus 로고    scopus 로고
    • Should we be worried about long-branch attraction in real data sets? : Investigations using metazoan 18S rRNA
    • Anderson F.E., and Swofford D.L. Should we be worried about long-branch attraction in real data sets? : Investigations using metazoan 18S rRNA. Mol. Phyl. Evol. 33 (2004) 440-451
    • (2004) Mol. Phyl. Evol. , vol.33 , pp. 440-451
    • Anderson, F.E.1    Swofford, D.L.2
  • 3
    • 22944471282 scopus 로고    scopus 로고
    • Evolutionary sequence analysis of complete eukaryotic genomes
    • Blair J.E., Shah P., and Hedges S.B. Evolutionary sequence analysis of complete eukaryotic genomes. BMC Bioinform. 6 (2005) 53
    • (2005) BMC Bioinform. , vol.6 , pp. 53
    • Blair, J.E.1    Shah, P.2    Hedges, S.B.3
  • 4
    • 33846491679 scopus 로고    scopus 로고
    • A phylogenomic study of human, dog, and mouse
    • 10.1371/journal.pcbi.0030002
    • Cannarozzi G., Schneider A., and Gonnet G. A phylogenomic study of human, dog, and mouse. PloS Comput. Biol. 3 1 (2007) e2 10.1371/journal.pcbi.0030002
    • (2007) PloS Comput. Biol. , vol.3 , Issue.1
    • Cannarozzi, G.1    Schneider, A.2    Gonnet, G.3
  • 5
    • 22844440801 scopus 로고    scopus 로고
    • The systematic component of phylogenetic error as a function of taxonomic sampling under parsimony
    • Debry R.W. The systematic component of phylogenetic error as a function of taxonomic sampling under parsimony. Syst. Biol. 54 (2005) 432-440
    • (2005) Syst. Biol. , vol.54 , pp. 432-440
    • Debry, R.W.1
  • 6
    • 0025064035 scopus 로고
    • The pattern of mammalian evolution and the relative rate of molecular evolution
    • Easteal S. The pattern of mammalian evolution and the relative rate of molecular evolution. Genetics 124 (1990) 165-173
    • (1990) Genetics , vol.124 , pp. 165-173
    • Easteal, S.1
  • 7
    • 30744460614 scopus 로고    scopus 로고
    • Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of Saccharomyces species
    • Fares N.A., Byrne K.P., and Wolfe K.H. Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of Saccharomyces species. Mol. Biol. Evol. 23 (2006) 245-253
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 245-253
    • Fares, N.A.1    Byrne, K.P.2    Wolfe, K.H.3
  • 8
    • 84959798530 scopus 로고
    • Cases in which parsimony and compatibility methods will be positively misleading
    • Felsenstein J. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27 (1978) 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. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (1985) 783-791
    • (1985) Evolution , vol.39 , pp. 783-791
    • Felsenstein, J.1
  • 10
    • 34548525654 scopus 로고    scopus 로고
    • Felsenstein, J., 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5, pp. 164-166.
  • 12
    • 0026911443 scopus 로고
    • Higher rates of amino acid substitution in rodents than in humans
    • Gu X., and Li W.-H. Higher rates of amino acid substitution in rodents than in humans. Mol. Phyl. Evol. 1 (1992) 211-214
    • (1992) Mol. Phyl. Evol. , vol.1 , pp. 211-214
    • Gu, X.1    Li, W.-H.2
  • 13
    • 0000084234 scopus 로고
    • A framework for the quantitative study of evolutionary trees
    • Hendy M.D., and Penny D. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38 (1989) 297-309
    • (1989) Syst. Zool. , vol.38 , pp. 297-309
    • Hendy, M.D.1    Penny, D.2
  • 14
    • 0032023889 scopus 로고    scopus 로고
    • Taxonomic sampling, phylogenetic accuracy, and investigator bias
    • Hillis D.M. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47 (1998) 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., Pollock D.D., McGuire J.A., and Zwickl D.J. Is sparse taxon sampling a problem for phylogenetic inference?. Syst. Biol. 52 (2003) 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
  • 17
    • 19044362395 scopus 로고    scopus 로고
    • Gene family content-based phylogeny of prokaryotes: the effect of criteria for inferring homology
    • Hughes A.L., Ekollu V., Friedman R., and Rose J.R. Gene family content-based phylogeny of prokaryotes: the effect of criteria for inferring homology. Syst. Biol. 54 (2005) 268-276
    • (2005) Syst. Biol. , vol.54 , pp. 268-276
    • Hughes, A.L.1    Ekollu, V.2    Friedman, R.3    Rose, J.R.4
  • 18
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones D.T., Taylor W.R., and Thornton J.M. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8 (1992) 275-282
    • (1992) Comput. Appl. Biosci. , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 19
    • 13844281341 scopus 로고    scopus 로고
    • Jørgensen, F.G., Hobolth, A., Hornshøj, H., Bendixen, C., Fredholm, M., Schierup, M.H., 2005. Comparative analysis of protein coding sequences from human, mouse, and the domesticated pig. BMC Biology 3, 2. doi:10.1186/1741-7007-3-2.
  • 20
    • 0034992826 scopus 로고    scopus 로고
    • The closest BLAST hit is often not the nearest neighbor
    • Koski L.B., and Golding G.B. The closest BLAST hit is often not the nearest neighbor. J. Mol. Evol. 52 (2001) 540-542
    • (2001) J. Mol. Evol. , vol.52 , pp. 540-542
    • Koski, L.B.1    Golding, G.B.2
  • 21
    • 3242810318 scopus 로고    scopus 로고
    • MEGA3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
    • Kumar S., Tamura K., and Nei M. MEGA3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief. Bioinform. 5 (2004) 150-163
    • (2004) Brief. Bioinform. , vol.5 , pp. 150-163
    • Kumar, S.1    Tamura, K.2    Nei, M.3
  • 22
    • 0025129816 scopus 로고
    • Molecular phylogeny of rodentia, lagomorpha, primates, artiodactyla, and carnivora and molecular clocks
    • Li W.-H., Gouy M., Sharp P.M., O'hUigin C., and Yang Y.-W. Molecular phylogeny of rodentia, lagomorpha, primates, artiodactyla, and carnivora and molecular clocks. Proc. Natl. Acad. Sci. USA 87 (1990) 6703-6707
    • (1990) Proc. Natl. Acad. Sci. USA , vol.87 , pp. 6703-6707
    • Li, W.-H.1    Gouy, M.2    Sharp, P.M.3    O'hUigin, C.4    Yang, Y.-W.5
  • 23
    • 0141832717 scopus 로고    scopus 로고
    • Revisting the glires concept - phylogenetic analysis of nuclear sequences
    • Misawa K., and Janke A. Revisting the glires concept - phylogenetic analysis of nuclear sequences. Mol. Phyl. Evol. 28 (2003) 320-327
    • (2003) Mol. Phyl. Evol. , vol.28 , pp. 320-327
    • Misawa, K.1    Janke, A.2
  • 24
    • 0344243515 scopus 로고    scopus 로고
    • Reanalysis of Murphy et al.'s data gives various mammalian phylogenies and suggests overcredibility of Bayesian trees
    • Misawa K., and Nei M. Reanalysis of Murphy et al.'s data gives various mammalian phylogenies and suggests overcredibility of Bayesian trees. J. Mol. Evol. 57 (2003) S290-S296
    • (2003) J. Mol. Evol. , vol.57
    • Misawa, K.1    Nei, M.2
  • 25
    • 0034350422 scopus 로고    scopus 로고
    • More taxa or more characters revisited: combining data from nuclear protein-encoding genes for phylogenetic analyses of Noctuoidea (Insecta: Lepidoptera)
    • Mitchell A., Mitter C., and Regier G.C. More taxa or more characters revisited: combining data from nuclear protein-encoding genes for phylogenetic analyses of Noctuoidea (Insecta: Lepidoptera). Syst. Biol. 49 (2000) 202-224
    • (2000) Syst. Biol. , vol.49 , pp. 202-224
    • Mitchell, A.1    Mitter, C.2    Regier, G.C.3
  • 28
    • 0032023887 scopus 로고    scopus 로고
    • Sensitivity of phylogeny estimation to taxonomic sampling
    • Poe S. Sensitivity of phylogeny estimation to taxonomic sampling. Syst. Biol. 47 (1998) 18-31
    • (1998) Syst. Biol. , vol.47 , pp. 18-31
    • Poe, S.1
  • 29
    • 0035722246 scopus 로고    scopus 로고
    • Biases in maximum likelihood and parsimony: a simulation approach to a 10-taxon case
    • Pol D., and Siddall M.E. Biases in maximum likelihood and parsimony: a simulation approach to a 10-taxon case. Cladistics 17 (2001) 266-281
    • (2001) Cladistics , vol.17 , pp. 266-281
    • Pol, D.1    Siddall, M.E.2
  • 30
    • 0036699885 scopus 로고    scopus 로고
    • Increased taxon sampling is advantageous for phylogenetic inference
    • Pollock D.D., Zwickl D.J., McGuire J.A., and Hillis D.M. Increased taxon sampling is advantageous for phylogenetic inference. Syst. Biol. 51 (2002) 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
  • 31
    • 0032225752 scopus 로고    scopus 로고
    • Taxon sampling and the accuracy of large phylogenies
    • Rannala B., Huelsenbeck J.P., Yang Z., and Nielsen R. Taxon sampling and the accuracy of large phylogenies. Syst. Biol. 47 (1998) 702-710
    • (1998) Syst. Biol. , vol.47 , pp. 702-710
    • Rannala, B.1    Huelsenbeck, J.P.2    Yang, Z.3    Nielsen, R.4
  • 32
    • 0035845536 scopus 로고    scopus 로고
    • Incomplete taxon sampling is not a problem for phylogenetic inference
    • Rosenberg M.S., and Kumar S. Incomplete taxon sampling is not a problem for phylogenetic inference. Proc. Natl. Acad. Sci. USA 58 (2001) 10751-10756
    • (2001) Proc. Natl. Acad. Sci. USA , vol.58 , pp. 10751-10756
    • Rosenberg, M.S.1    Kumar, S.2
  • 33
    • 0037291976 scopus 로고    scopus 로고
    • Taxon sampling, bioinformatics, and phylogenomics
    • Rosenberg M.S., and Kumar S. Taxon sampling, bioinformatics, and phylogenomics. Syst. Biol. 52 (2003) 119-124
    • (2003) Syst. Biol. , vol.52 , pp. 119-124
    • Rosenberg, M.S.1    Kumar, S.2
  • 34
    • 0029836454 scopus 로고    scopus 로고
    • Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies
    • Strimmer K., and von Haeseler A. Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13 (1996) 964-969
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 964-969
    • Strimmer, K.1    von Haeseler, A.2
  • 35
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
    • (1997) Nucleic Acids Res. , vol.25 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 36
    • 0029878719 scopus 로고    scopus 로고
    • Phylogenetic analysis using parsimony and likelihood methods
    • Yang Z. Phylogenetic analysis using parsimony and likelihood methods. J. Mol. Evol. 42 (1996) 294-307
    • (1996) J. Mol. Evol. , vol.42 , pp. 294-307
    • Yang, Z.1
  • 37
    • 0036699481 scopus 로고    scopus 로고
    • Increased taxon sampling greatly reduces phylogenetic error
    • Zwickl D.J., and Hillis D.M. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 51 (2002) 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.