메뉴 건너뛰기




Volumn 35, Issue 3, 2010, Pages 429-448

When phylogenetic assumptions are violated: Base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics

Author keywords

[No Author keywords available]

Indexed keywords

BAYESIAN ANALYSIS; BEETLE; DATA SET; EVOLUTIONARY BIOLOGY; GENOME; HETEROGENEITY; MOLECULAR ANALYSIS; PARSIMONY ANALYSIS; PHYLOGENETICS; PHYLOGENY;

EID: 78649873812     PISSN: 03076970     EISSN: 13653113     Source Type: Journal    
DOI: 10.1111/j.1365-3113.2009.00517.x     Document Type: Article
Times cited : (123)

References (106)
  • 1
    • 33646892649 scopus 로고    scopus 로고
    • Matchedpairs tests of homogeneity with applications to homologous nucleotide sequences
    • Ababneh, F., Jermiin, L.S., Ma, C. & Robinson, J. (2006) Matchedpairs tests of homogeneity with applications to homologous nucleotide sequences. Bioinformatics, 22, 1225-1231.
    • (2006) Bioinformatics , vol.22 , pp. 1225-1231
    • Ababneh, F.1    Jermiin, L.S.2    Ma, C.3    Robinson, J.4
  • 2
    • 0031371067 scopus 로고    scopus 로고
    • Multiple sources of character information and the phylogeny of Hawaiian Drosophilids
    • Baker, R.H. & DeSalle, R. (1997) Multiple sources of character information and the phylogeny of Hawaiian Drosophilids. Systematic Biology, 46, 654-673.
    • (1997) Systematic Biology , vol.46 , pp. 654-673
    • Baker, R.H.1    DeSalle, R.2
  • 3
    • 84972510219 scopus 로고
    • Statistical analysis of hominoid molecular evolution
    • Barry, D. & Hartigan, J.A. (1987) Statistical analysis of hominoid molecular evolution. Statistical Science, 2, 191-210.
    • (1987) Statistical Science , vol.2 , pp. 191-210
    • Barry, D.1    Hartigan, J.A.2
  • 4
    • 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
  • 5
    • 84981636358 scopus 로고
    • Phylogenetic analysis of Adephaga (Coleoptera) based on characters of the larval head
    • Beutel, R.G. (1993) Phylogenetic analysis of Adephaga (Coleoptera) based on characters of the larval head. Systematic Entomology, 18, 127-147.
    • (1993) Systematic Entomology , vol.18 , pp. 127-147
    • Beutel, R.G.1
  • 6
    • 0034480303 scopus 로고    scopus 로고
    • Phylogenetic relationships of the suborders of Coleoptera (Insecta)
    • Beutel, R.G. & Haas, F. (2000) Phylogenetic relationships of the suborders of Coleoptera (Insecta). Cladistics, 16, 103-141.
    • (2000) Cladistics , vol.16 , pp. 103-141
    • Beutel, R.G.1    Haas, F.2
  • 7
    • 34848827693 scopus 로고    scopus 로고
    • Molecular phylogenetics of Elateriformia (Coleoptera): evolution of bioluminescence and neoteny
    • Bocakova, M., Bocak, L., Hunt, T., Teraväinen, M. & Vogler, A.P. (2007) Molecular phylogenetics of Elateriformia (Coleoptera): evolution of bioluminescence and neoteny. Cladistics, 23, 477-496.
    • (2007) Cladistics , vol.23 , pp. 477-496
    • Bocakova, M.1    Bocak, L.2    Hunt, T.3    Teraväinen, M.4    Vogler, A.P.5
  • 8
    • 0033561361 scopus 로고    scopus 로고
    • Animal mitochondrial genomes
    • Boore, J.L. (1999) Animal mitochondrial genomes. Nucleic Acids Research, 27, 1767-1780.
    • (1999) Nucleic Acids Research , vol.27 , pp. 1767-1780
    • Boore, J.L.1
  • 9
    • 0031769998 scopus 로고    scopus 로고
    • Big trees from little genomes: mitochondrial gene order as a phylogenetic tool
    • Boore, J.L. & Brown, W.M. (1998) Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Current Opinion in Genetics and Development, 8, 668-674.
    • (1998) Current Opinion in Genetics and Development , vol.8 , pp. 668-674
    • Boore, J.L.1    Brown, W.M.2
  • 10
    • 0028976102 scopus 로고
    • Deducing the pattern of arthropod phylogeny from mitochondrial DNA rearrangements
    • Boore, J.L., Collins, T.M., Stanton, D., Daehler, L.L. & Brown, W.M. (1995) Deducing the pattern of arthropod phylogeny from mitochondrial DNA rearrangements. Nature, 376, 163-165.
    • (1995) Nature , vol.376 , pp. 163-165
    • Boore, J.L.1    Collins, T.M.2    Stanton, D.3    Daehler, L.L.4    Brown, W.M.5
  • 11
    • 0032537194 scopus 로고    scopus 로고
    • Gene translocation links insects and crustaceans
    • Boore, J.L., Lavrov, D.V. & Brown, W.M. (1998) Gene translocation links insects and crustaceans. Nature, 392, 667-668.
    • (1998) Nature , vol.392 , pp. 667-668
    • Boore, J.L.1    Lavrov, D.V.2    Brown, W.M.3
  • 12
    • 0035694055 scopus 로고    scopus 로고
    • The evolution of bioluminescence in cantharoids (Coleoptera: Elateroidea)
    • Branham, M.A. & Wenzel, J.W. (2001) The evolution of bioluminescence in cantharoids (Coleoptera: Elateroidea). Florida Entomologist, 84, 565-586.
    • (2001) Florida Entomologist , vol.84 , pp. 565-586
    • Branham, M.A.1    Wenzel, J.W.2
  • 13
    • 43949160320 scopus 로고
    • Branch support and tree stability
    • Bremer, K. (1994) Branch support and tree stability. Cladistics, 10, 295-304.
    • (1994) Cladistics , vol.10 , pp. 295-304
    • Bremer, K.1
  • 14
    • 37549067395 scopus 로고    scopus 로고
    • The complete mitochondrial genome of the tobacco hornworm, Manduca sexta, (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths
    • Cameron, S.L. & Whiting, M.F. (2008) The complete mitochondrial genome of the tobacco hornworm, Manduca sexta, (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths. Gene, 408, 112-123.
    • (2008) Gene , vol.408 , pp. 112-123
    • Cameron, S.L.1    Whiting, M.F.2
  • 15
    • 13544270058 scopus 로고    scopus 로고
    • Mitochondrial genome data alone are not enough to unambiguously resolve the relationships of Entognatha, Insecta and Crustacea sensu lato (Athropoda)
    • Cameron, S.L., Miller, K.B., D'Haese, C.A., Whiting, M.F. & Barker, S.C. (2004) Mitochondrial genome data alone are not enough to unambiguously resolve the relationships of Entognatha, Insecta and Crustacea sensu lato (Athropoda). Cladistics, 20, 534-557.
    • (2004) Cladistics , vol.20 , pp. 534-557
    • Cameron, S.L.1    Miller, K.B.2    D'Haese, C.A.3    Whiting, M.F.4    Barker, S.C.5
  • 17
    • 33845866870 scopus 로고    scopus 로고
    • A mitochondrial genome phylogeny of Diptera: whole genome sequence data accurately resolve relationships over broad timescales with high precision
    • Cameron, S.L., Lambkin, C.L., Barker, S.C. & Whiting, M.F. (2007) A mitochondrial genome phylogeny of Diptera: whole genome sequence data accurately resolve relationships over broad timescales with high precision. Systematic Entomology, 32, 40-59.
    • (2007) Systematic Entomology , vol.32 , pp. 40-59
    • Cameron, S.L.1    Lambkin, C.L.2    Barker, S.C.3    Whiting, M.F.4
  • 18
    • 55049131972 scopus 로고    scopus 로고
    • The sequence of the mitochondrial genomes of two vespid wasps reveals a number of derived tRNA gene rearrangements
    • Cameron, S.L., Dowton, M., Castro, L.R. et al., (2008) The sequence of the mitochondrial genomes of two vespid wasps reveals a number of derived tRNA gene rearrangements. Genome, 51, 800-808.
    • (2008) Genome , vol.51 , pp. 800-808
    • Cameron, S.L.1    Dowton, M.2    Castro, L.R.3
  • 19
    • 33845789114 scopus 로고    scopus 로고
    • Mitochondrial genomes in the Hymenoptera and their utility as phylogenetic markers
    • Castro, L.R. & Dowton, M. (2007) Mitochondrial genomes in the Hymenoptera and their utility as phylogenetic markers. Systematic Entomology, 32, 60-69.
    • (2007) Systematic Entomology , vol.32 , pp. 60-69
    • Castro, L.R.1    Dowton, M.2
  • 20
    • 0036167319 scopus 로고    scopus 로고
    • Basal relationships of Coleoptera inferred from 18S rDNA sequences
    • Caterino, M.S., Shull, V.L., Hammond, P.M. & Vogler, A.P. (2002) Basal relationships of Coleoptera inferred from 18S rDNA sequences. Zoologica Scripta, 31, 41-49.
    • (2002) Zoologica Scripta , vol.31 , pp. 41-49
    • Caterino, M.S.1    Shull, V.L.2    Hammond, P.M.3    Vogler, A.P.4
  • 21
    • 15944406867 scopus 로고    scopus 로고
    • On the constitution and phylogeny of Staphyliniformia (Insecta: Coleoptera)
    • Caterino, M.S., Hunt, T. & Vogler, A.P. (2005) On the constitution and phylogeny of Staphyliniformia (Insecta: Coleoptera). Molecular Phylogenetics and Evolution, 34, 655-672.
    • (2005) Molecular Phylogenetics and Evolution , vol.34 , pp. 655-672
    • Caterino, M.S.1    Hunt, T.2    Vogler, A.P.3
  • 22
    • 0001111484 scopus 로고
    • The phylogenetic significance of ommatidium structure in the compound eyes of polyphagan beetles
    • Caveney, S. (1986) The phylogenetic significance of ommatidium structure in the compound eyes of polyphagan beetles. Canadian Journal of Zoology/Revue Canadienne de Zoologie, 64, 1787-1819.
    • (1986) Canadian Journal of Zoology/Revue Canadienne de Zoologie , vol.64 , pp. 1787-1819
    • Caveney, S.1
  • 23
    • 12044252488 scopus 로고
    • Compositional bias, character-state bias, and character-state reconstruction using parsimony
    • Collins, T.M., Wimberger, P.H. & Naylor, G.J.P. (1994) Compositional bias, character-state bias, and character-state reconstruction using parsimony. Systematic Biology, 43, 482-496.
    • (1994) Systematic Biology , vol.43 , pp. 482-496
    • Collins, T.M.1    Wimberger, P.H.2    Naylor, G.J.P.3
  • 25
    • 0141685723 scopus 로고    scopus 로고
    • Comment of "Hexapod origins: Monophyletic or paraphyletic?"
    • Delsuc, F., Philips, M.J. & Penny, D. (2003) Comment of "Hexapod origins: Monophyletic or paraphyletic?". Science, 301, 1482e.
    • (2003) Science , vol.301
    • Delsuc, F.1    Philips, M.J.2    Penny, D.3
  • 26
    • 17744394753 scopus 로고    scopus 로고
    • Phylogenomics and the reconstruction of the tree of life
    • Delsuc, F., Brinkmann, H. & Philippe, H. (2005) Phylogenomics and the reconstruction of the tree of life. Nature Reviews: Genetics, 6, 361-375.
    • (2005) Nature Reviews: Genetics , vol.6 , pp. 361-375
    • Delsuc, F.1    Brinkmann, H.2    Philippe, H.3
  • 27
    • 33644536713 scopus 로고    scopus 로고
    • Tunicates and not cephalochordates are the closest living relatives of vertabrates
    • Delsuc, F., Brinkmann, H., Chourrout, D. & Philippe, H. (2006) Tunicates and not cephalochordates are the closest living relatives of vertabrates. Nature, 439, 965-968.
    • (2006) Nature , vol.439 , pp. 965-968
    • Delsuc, F.1    Brinkmann, H.2    Chourrout, D.3    Philippe, H.4
  • 28
    • 0030641380 scopus 로고    scopus 로고
    • The evolution of strand-specific compositional bias. A case study in the hymenopteran mitochondrial 16S rRNA gene
    • Dowton, M. & Austin, A.D. (1997) The evolution of strand-specific compositional bias. A case study in the hymenopteran mitochondrial 16S rRNA gene. Molecular Biology and Evolution, 14, 109-112.
    • (1997) Molecular Biology and Evolution , vol.14 , pp. 109-112
    • Dowton, M.1    Austin, A.D.2
  • 29
    • 0033062252 scopus 로고    scopus 로고
    • Evolutionary dynamics of a mitochondrial rearrangement "hot spot" in the Hymenoptera
    • Dowton, M. & Austin, A.D. (1999) Evolutionary dynamics of a mitochondrial rearrangement "hot spot" in the Hymenoptera. Molecular Biology and Evolution, 16, 298-309.
    • (1999) Molecular Biology and Evolution , vol.16 , pp. 298-309
    • Dowton, M.1    Austin, A.D.2
  • 30
    • 0036408378 scopus 로고    scopus 로고
    • Mitochondrial gene rearrangements as phylogenetic characters in the invertebrates: the examination of genome 'morphology'
    • Dowton, M., Castro, L.R. & Austin, A.D. (2002) Mitochondrial gene rearrangements as phylogenetic characters in the invertebrates: the examination of genome 'morphology'. Invertebrate Systematics, 16, 345-356.
    • (2002) Invertebrate Systematics , vol.16 , pp. 345-356
    • Dowton, M.1    Castro, L.R.2    Austin, A.D.3
  • 31
    • 67349206083 scopus 로고    scopus 로고
    • Phylogenetic approaches for the analysis of mitochondrial genome sequence data in the Hymenoptera -a lineage with both rapidly and slowly evolving mitochondrial genomes
    • Dowton, M., Cameron, S.L., Austin, A.D. & Whiting, M.F. (2009) Phylogenetic approaches for the analysis of mitochondrial genome sequence data in the Hymenoptera -a lineage with both rapidly and slowly evolving mitochondrial genomes. Molecular Phylogenetics and Evolution, 52, 512-519.
    • (2009) Molecular Phylogenetics and Evolution , vol.52 , pp. 512-519
    • Dowton, M.1    Cameron, S.L.2    Austin, A.D.3    Whiting, M.F.4
  • 32
    • 42149157760 scopus 로고    scopus 로고
    • Broad phylogenomic sampling improves resolution of the animal tree of life
    • Dunn, C.W., Hejnol, A., Matus, D.Q., et al. (2008) Broad phylogenomic sampling improves resolution of the animal tree of life. Nature, 452, 745-749.
    • (2008) Nature , vol.452 , pp. 745-749
    • Dunn, C.W.1    Hejnol, A.2    Matus, D.Q.3
  • 33
    • 0028272315 scopus 로고
    • RNA sequence analysis using covariance models
    • Eddy, S.R. & Durbin, R. (1994) RNA sequence analysis using covariance models. Nucleic Acids Research, 22, 2079-2088.
    • (1994) Nucleic Acids Research , vol.22 , pp. 2079-2088
    • Eddy, S.R.1    Durbin, R.2
  • 34
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792-1797.
    • (2004) Nucleic Acids Research , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 35
    • 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. Systematic Zoology, 27, 401-410.
    • (1978) Systematic Zoology , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 36
    • 0034818755 scopus 로고    scopus 로고
    • Taking variation of evolutionary rates between sites in account in inferring phylogenies
    • Felsenstein, J. (2001) Taking variation of evolutionary rates between sites in account in inferring phylogenies. Journal of Molecular Evolution, 53, 447-455.
    • (2001) Journal of Molecular Evolution , vol.53 , pp. 447-455
    • Felsenstein, J.1
  • 37
    • 52049118280 scopus 로고    scopus 로고
    • A mitochondrial genome phylogeny of Orthoptera (Insecta) and approaches to maximizing phylogenetic signal found within mitochondrial genome data
    • Fenn, J.D., Song, H., Cameron, S.L. & Whiting, M.F. (2008) A mitochondrial genome phylogeny of Orthoptera (Insecta) and approaches to maximizing phylogenetic signal found within mitochondrial genome data. Molecular Phylogenetics and Evolution, 49, 59-68.
    • (2008) Molecular Phylogenetics and Evolution , vol.49 , pp. 59-68
    • Fenn, J.D.1    Song, H.2    Cameron, S.L.3    Whiting, M.F.4
  • 38
    • 0014092973 scopus 로고
    • A method for estimating the number of invariant amino acid coding positions in a gene using cytochrome c as a model case
    • Fitch, W.M. & Margoliash, E. (1967) A method for estimating the number of invariant amino acid coding positions in a gene using cytochrome c as a model case. Biochemical Genetics, 1, 65-71.
    • (1967) Biochemical Genetics , vol.1 , pp. 65-71
    • Fitch, W.M.1    Margoliash, E.2
  • 39
    • 3242701529 scopus 로고    scopus 로고
    • Modeling compositional heterogeneity
    • Foster, P.G. (2004) Modeling compositional heterogeneity. Systematic Biology, 53, 485-495.
    • (2004) Systematic Biology , vol.53 , pp. 485-495
    • Foster, P.G.1
  • 40
    • 0033004743 scopus 로고    scopus 로고
    • Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions
    • Foster, P.G. & Hickey, D.A. (1999) Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. Journal of Molecular Evolution, 48, 284-290.
    • (1999) Journal of Molecular Evolution , vol.48 , pp. 284-290
    • Foster, P.G.1    Hickey, D.A.2
  • 42
    • 0031829758 scopus 로고    scopus 로고
    • Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis
    • Galtier, N. & Gouy, M. (1998) Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Molecular Biology and Evolution, 15, 871-879.
    • (1998) Molecular Biology and Evolution , vol.15 , pp. 871-879
    • Galtier, N.1    Gouy, M.2
  • 43
    • 12344282043 scopus 로고    scopus 로고
    • A comprehensive analysis of mammalian mitochondrial genome base composition and improved phylogenetic methods
    • Gibson, A., Gowri-Shankar, V., Higgs, P.G. & Rattray, M. (2005) A comprehensive analysis of mammalian mitochondrial genome base composition and improved phylogenetic methods. Molecular Biology and Evolution, 22, 251-264.
    • (2005) Molecular Biology and Evolution , vol.22 , pp. 251-264
    • Gibson, A.1    Gowri-Shankar, V.2    Higgs, P.G.3    Rattray, M.4
  • 44
    • 33750442556 scopus 로고    scopus 로고
    • Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization and retrotransposable elements
    • Gillespie, J.J., Johnston, J.S., Cannone, J.J. & Gutell, R.R. (2006) Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization and retrotransposable elements. Insect Molecular Biology, 15, 657-686.
    • (2006) Insect Molecular Biology , vol.15 , pp. 657-686
    • Gillespie, J.J.1    Johnston, J.S.2    Cannone, J.J.3    Gutell, R.R.4
  • 45
    • 0033499153 scopus 로고    scopus 로고
    • Analyzing large data sets in reasonable times: solutions for composite optima
    • Goloboff, P.A. (1999) Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics, 15, 415-428.
    • (1999) Cladistics , vol.15 , pp. 415-428
    • Goloboff, P.A.1
  • 47
    • 30744437133 scopus 로고    scopus 로고
    • On the correlation between composition and site-specific evolutionary rate: Implications for phylogenetic inference
    • Gowri-Shankar, V. & Rattray, M. (2006) On the correlation between composition and site-specific evolutionary rate: Implications for phylogenetic inference. Molecular Biology and Evolution, 23, 352-364.
    • (2006) Molecular Biology and Evolution , vol.23 , pp. 352-364
    • Gowri-Shankar, V.1    Rattray, M.2
  • 48
    • 34548074524 scopus 로고    scopus 로고
    • A reversible jump method for Bayesian phylogenetic inference with a non-homogeneous substitution model
    • Gowri-Shankar, V. & Rattray, M. (2007) A reversible jump method for Bayesian phylogenetic inference with a non-homogeneous substitution model. Molecular Biology and Evolution, 24, 1286-1299.
    • (2007) Molecular Biology and Evolution , vol.24 , pp. 1286-1299
    • Gowri-Shankar, V.1    Rattray, M.2
  • 49
    • 34247616059 scopus 로고    scopus 로고
    • Base-compositional heterogeneity in the RAG1 locus among didelphid marsupials: implications for phylogenetic inference and the evolution of GC content
    • Gruber, K.F., Voss, R.S. & Jansa, S.A. (2007) Base-compositional heterogeneity in the RAG1 locus among didelphid marsupials: implications for phylogenetic inference and the evolution of GC content. Systematic Biology, 56, 83-96.
    • (2007) Systematic Biology , vol.56 , pp. 83-96
    • Gruber, K.F.1    Voss, R.S.2    Jansa, S.A.3
  • 50
    • 0027463557 scopus 로고
    • Ribosomal RNA trees misleading?
    • Hasegawa, M. & Hashimoto, T. (1993) Ribosomal RNA trees misleading? Nature, 361, 23.
    • (1993) Nature , vol.361 , pp. 23
    • Hasegawa, M.1    Hashimoto, T.2
  • 51
    • 4644252702 scopus 로고    scopus 로고
    • Tracing the decay of the historical signal in biological sequence data
    • Ho, J.W.K. & Jermiin, L.S. (2004) Tracing the decay of the historical signal in biological sequence data. Systematic Biology, 53, 623-637.
    • (2004) Systematic Biology , vol.53 , pp. 623-637
    • Ho, J.W.K.1    Jermiin, L.S.2
  • 52
    • 33748650992 scopus 로고    scopus 로고
    • SeqVis: Visualization of compositional heterogeneity in large alignments of nucleotides
    • Ho, J.W.K., Adams, C.E., Lew, J.B., et al. (2006) SeqVis: Visualization of compositional heterogeneity in large alignments of nucleotides. Bioinformatics, 22, 2162-2163.
    • (2006) Bioinformatics , vol.22 , pp. 2162-2163
    • Ho, J.W.K.1    Adams, C.E.2    Lew, J.B.3
  • 53
    • 0023413051 scopus 로고
    • Origin and evolution of organisms as deduced from 5S ribosomal RNA sequences
    • Hori, H. & Osawa, S. (1987) Origin and evolution of organisms as deduced from 5S ribosomal RNA sequences. Molecular Biology and Evolution, 4, 445-472.
    • (1987) Molecular Biology and Evolution , vol.4 , pp. 445-472
    • Hori, H.1    Osawa, S.2
  • 54
    • 30744435829 scopus 로고    scopus 로고
    • Dense taxonomic EST sampling and its applications for molecular systematics of the Coleoptera (Beetles)
    • Hughes, J., Longhorn, S.J., Papadopoulou, A., et al. (2006) Dense taxonomic EST sampling and its applications for molecular systematics of the Coleoptera (Beetles). Molecular Biology and Evolution, 23, 268-278.
    • (2006) Molecular Biology and Evolution , vol.23 , pp. 268-278
    • Hughes, J.1    Longhorn, S.J.2    Papadopoulou, A.3
  • 55
    • 37549050969 scopus 로고    scopus 로고
    • A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation
    • Hunt, T., Bergsten, J., Levkanicova, Z., et al. (2007) A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation. Science, 318, 1913-1916.
    • (2007) Science , vol.318 , pp. 1913-1916
    • Hunt, T.1    Bergsten, J.2    Levkanicova, Z.3
  • 58
    • 33947532595 scopus 로고    scopus 로고
    • Estimation of phylogeny and invariant sites under the general Markov model of nucleotide sequence evolution
    • Jayaswal, V., Robinson, J. & Jermiin, L.S. (2007) Estimation of phylogeny and invariant sites under the general Markov model of nucleotide sequence evolution. Systematic Biology, 56, 155-162.
    • (2007) Systematic Biology , vol.56 , pp. 155-162
    • Jayaswal, V.1    Robinson, J.2    Jermiin, L.S.3
  • 59
    • 4644299089 scopus 로고    scopus 로고
    • The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated
    • Jermiin, L.S., Ho, S.Y., Ababneh, F., Robinson, J. & Larkum, A.W. (2004) The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated. Systematic Biology, 53, 638-643.
    • (2004) Systematic Biology , vol.53 , pp. 638-643
    • Jermiin, L.S.1    Ho, S.Y.2    Ababneh, F.3    Robinson, J.4    Larkum, A.W.5
  • 61
    • 68049128028 scopus 로고    scopus 로고
    • SeqVis: A tool for detecting compositional heterogeneity among aligned nucleotide sequences
    • (ed. by D. Posada). Humana Press, Totowa, New Jersey
    • Jermiin, L.S., Ho, J.W.K., Lau, K.W. & Jayaswal, V. (2009) SeqVis: A tool for detecting compositional heterogeneity among aligned nucleotide sequences. Bioinformatics for DNA Sequence Analysis (ed. by D. Posada), pp. 65-91. Humana Press, Totowa, New Jersey.
    • (2009) Bioinformatics for DNA Sequence Analysis , pp. 65-91
    • Jermiin, L.S.1    Ho, J.W.K.2    Lau, K.W.3    Jayaswal, V.4
  • 63
    • 0001917382 scopus 로고
    • A systematic review of amphizoid beetles (Amphizoidae: Coleoptera) and their phylogenetic relationships to other Adephaga
    • Kavanaugh, D.H. (1986) A systematic review of amphizoid beetles (Amphizoidae: Coleoptera) and their phylogenetic relationships to other Adephaga. Proceedings of the California Academy of Sciences, 44, 67-109.
    • (1986) Proceedings of the California Academy of Sciences , vol.44 , pp. 67-109
    • Kavanaugh, D.H.1
  • 64
    • 7244221755 scopus 로고    scopus 로고
    • Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous
    • Kolaczkowski, B. & Thorton, J.W. (2004) Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature, 431, 980-984.
    • (2004) Nature , vol.431 , pp. 980-984
    • Kolaczkowski, B.1    Thorton, J.W.2
  • 66
    • 0034923337 scopus 로고    scopus 로고
    • Disparity index: a simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences
    • Kumar, S. & Gadagkar, S.R. (2001) Disparity index: a simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences. Genetics, 158, 1321-1327.
    • (2001) Genetics , vol.158 , pp. 1321-1327
    • Kumar, S.1    Gadagkar, S.R.2
  • 70
    • 0030966808 scopus 로고    scopus 로고
    • Evolutionary shifts in three major structural features of the mitochondrial genome among iguanian lizards
    • Macey, J.R., Larson, A., Ananjeva, N.B. & Papenfuss, T.J. (1997) Evolutionary shifts in three major structural features of the mitochondrial genome among iguanian lizards. Journal of Molecular Evolution, 44, 660-674.
    • (1997) Journal of Molecular Evolution , vol.44 , pp. 660-674
    • Macey, J.R.1    Larson, A.2    Ananjeva, N.B.3    Papenfuss, T.J.4
  • 71
    • 0003821327 scopus 로고    scopus 로고
    • Sinauer Associates, Inc., Sunderland, Massachusetts
    • Maddison, D.R. & Maddison, W.P. (2005) MacClade 4. Sinauer Associates, Inc., Sunderland, Massachusetts.
    • (2005) MacClade 4
    • Maddison, D.R.1    Maddison, W.P.2
  • 72
    • 0001705679 scopus 로고    scopus 로고
    • Phylogeny of carabid beetles as inferred from 18S ribosomal DNA (Coleoptera: Carabidae)
    • Maddison, D.R., Baker, M.D. & Ober, K.A. (1999) Phylogeny of carabid beetles as inferred from 18S ribosomal DNA (Coleoptera: Carabidae). Systematic Entomology, 24, 103-138.
    • (1999) Systematic Entomology , vol.24 , pp. 103-138
    • Maddison, D.R.1    Baker, M.D.2    Ober, K.A.3
  • 73
    • 27544508958 scopus 로고    scopus 로고
    • A gamma mixture model better accounts for among site rate heterogeneity
    • Mayrose, I., Friedman, N. & Pupko, T. (2005) A gamma mixture model better accounts for among site rate heterogeneity. Bioinformatics, 21 (Suppl. 2), ii151-ii158.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 2
    • Mayrose, I.1    Friedman, N.2    Pupko, T.3
  • 74
    • 0034932095 scopus 로고    scopus 로고
    • The complete mitochondrial DNA sequence of the basal hexapod Tetrodontophora bielanensis: Evidence for heteroplasmy and tRNA translocations
    • Nardi, F., Carapelli, A., Fanciulli, P.P., Dallai, R. & Frati, F. (2001) The complete mitochondrial DNA sequence of the basal hexapod Tetrodontophora bielanensis: Evidence for heteroplasmy and tRNA translocations. Molecular Biology and Evolution, 18, 1293-1304.
    • (2001) Molecular Biology and Evolution , vol.18 , pp. 1293-1304
    • Nardi, F.1    Carapelli, A.2    Fanciulli, P.P.3    Dallai, R.4    Frati, F.5
  • 77
    • 0033504552 scopus 로고    scopus 로고
    • The parsimony ratchet, a new method for rapid parsimony analysis
    • Nixon, K.C. (1999) The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics, 15, 407-414.
    • (1999) Cladistics , vol.15 , pp. 407-414
    • Nixon, K.C.1
  • 78
    • 82955179234 scopus 로고    scopus 로고
    • MrModeltest v.2
    • Evolutionary Biology Centre, Uppsala University, Uppsala
    • Nylander, J.A.A. (2004) MrModeltest v.2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University, Uppsala.
    • (2004) Program distributed by the author
    • Nylander, J.A.A.1
  • 80
    • 33749516796 scopus 로고    scopus 로고
    • Large-scale sequencing and the new animal phylogeny
    • Philippe, H. & Telford, M.J. (2005) Large-scale sequencing and the new animal phylogeny. Trends in Ecology and Evolution, 21, 614-620.
    • (2005) Trends in Ecology and Evolution , vol.21 , pp. 614-620
    • Philippe, H.1    Telford, M.J.2
  • 83
    • 3042550872 scopus 로고    scopus 로고
    • Genome-scale phylogeny and the detection of systematic biases
    • Phillips, M.J., Delsuc, F. & Penny, D. (2004) Genome-scale phylogeny and the detection of systematic biases. Molecular Biology and Evolution, 21, 1455-1458.
    • (2004) Molecular Biology and Evolution , vol.21 , pp. 1455-1458
    • Phillips, M.J.1    Delsuc, F.2    Penny, D.3
  • 85
    • 9644301241 scopus 로고    scopus 로고
    • Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests
    • Posada, D. & Buckley, T.R. (2004) Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests. Systematic Biology, 53, 793-808.
    • (2004) Systematic Biology , vol.53 , pp. 793-808
    • Posada, D.1    Buckley, T.R.2
  • 86
    • 0026808975 scopus 로고
    • Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA
    • Reeves, J.H. (1992) Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA. Journal of Molecular Evolution, 35, 17-31.
    • (1992) Journal of Molecular Evolution , vol.35 , pp. 17-31
    • Reeves, J.H.1
  • 87
    • 29344441657 scopus 로고    scopus 로고
    • Animal evolution and the molecular signature of radiations compressed in time
    • Rokas, A., Krüger, D. & Carroll, S.B. (2005) Animal evolution and the molecular signature of radiations compressed in time. Science, 310, 1933-1938.
    • (2005) Science , vol.310 , pp. 1933-1938
    • Rokas, A.1    Krüger, D.2    Carroll, S.B.3
  • 88
    • 0035153070 scopus 로고    scopus 로고
    • Pyrosequencing sheds light on DNA sequencing
    • Ronaghi, M. (2001) Pyrosequencing sheds light on DNA sequencing. Genome Research, 11, 3-11.
    • (2001) Genome Research , vol.11 , pp. 3-11
    • Ronaghi, M.1
  • 89
    • 0041386108 scopus 로고    scopus 로고
    • MRBAYES 3: Bayesian phylogenetic inference under mixed models
    • Ronquist, F. & Huelsenbeck, J.P. (2003) MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574.
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 90
    • 70349434888 scopus 로고    scopus 로고
    • Nonstationary evolution and compositional heterogeneity in beetle mitochondrial phylogenomics
    • Sheffield, N.C., Song, H., Cameron, S.L. & Whiting, M.F. (2009) Nonstationary evolution and compositional heterogeneity in beetle mitochondrial phylogenomics. Systematic Biology, 58, 381-394.
    • (2009) Systematic Biology , vol.58 , pp. 381-394
    • Sheffield, N.C.1    Song, H.2    Cameron, S.L.3    Whiting, M.F.4
  • 91
    • 0035527399 scopus 로고    scopus 로고
    • Sequence alignment of 18S ribosomal RNA and the basal relationships of adephagan beetles: Evidence for monophyly of aquatic families and the placement of Trachypachidae
    • Shull, V.L., Vogler, A.P., Baker, M.D., Maddison, D.R. & Hammond, P.M. (2001) Sequence alignment of 18S ribosomal RNA and the basal relationships of adephagan beetles: Evidence for monophyly of aquatic families and the placement of Trachypachidae. Systematic Biology, 50, 945-969.
    • (2001) Systematic Biology , vol.50 , pp. 945-969
    • Shull, V.L.1    Vogler, A.P.2    Baker, M.D.3    Maddison, D.R.4    Hammond, P.M.5
  • 94
    • 34347169150 scopus 로고
    • Bau und Bedeutung der malpighischen Gefässe der Coleopteren
    • Stammer, H.J. (1934) Bau und Bedeutung der malpighischen Gefässe der Coleopteren. Zoomorphology, 29, 196-217.
    • (1934) Zoomorphology , vol.29 , pp. 196-217
    • Stammer, H.J.1
  • 95
    • 0034350429 scopus 로고    scopus 로고
    • Invariable sites models and their use in phylogeny reconstruction
    • Steel, M., Huson, D. & Lockhart, P.J. (2000) Invariable sites models and their use in phylogeny reconstruction. Systematic Biology, 49, 225-232.
    • (2000) Systematic Biology , vol.49 , pp. 225-232
    • Steel, M.1    Huson, D.2    Lockhart, P.J.3
  • 96
    • 0037353318 scopus 로고    scopus 로고
    • Phylogenetic and genomic analysis of the complete mitochondrial DNA sequence of the spotted asparagus beetle Crioceris duodecimpunctata
    • Stewart, J.B. & Beckenbach, A.T. (2003) Phylogenetic and genomic analysis of the complete mitochondrial DNA sequence of the spotted asparagus beetle Crioceris duodecimpunctata. Molecular Phylogenetics and Evolution, 26, 513-526.
    • (2003) Molecular Phylogenetics and Evolution , vol.26 , pp. 513-526
    • Stewart, J.B.1    Beckenbach, A.T.2
  • 99
    • 0033060854 scopus 로고    scopus 로고
    • The mitochondrial genome: structure, transcription, translation and replication
    • Taanman, J.W. (1999) The mitochondrial genome: structure, transcription, translation and replication. Biochimica et Biophysica Acta, 1410, 103-123.
    • (1999) Biochimica et Biophysica Acta , vol.1410 , pp. 103-123
    • Taanman, J.W.1
  • 100
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    • Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24, 1596.
    • (2007) Molecular Biology and Evolution , vol.24 , pp. 1596
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 101
    • 0034907489 scopus 로고    scopus 로고
    • Shared nucleotide composition biases among species and their impact on phylogenetic reconstructions of the Drosophilidae
    • Tarrío, R., Rodríguez-Trelles, F. & Ayala, F.J. (2001) Shared nucleotide composition biases among species and their impact on phylogenetic reconstructions of the Drosophilidae. Molecular Biology and Evolution, 18, 1464-1473.
    • (2001) Molecular Biology and Evolution , vol.18 , pp. 1464-1473
    • Tarrío, R.1    Rodríguez-Trelles, F.2    Ayala, F.J.3
  • 102
    • 0039694551 scopus 로고
    • Vergleichende Analyse der feinstrukturellen Organisation offener Rhabdome in den Augen der Cucujiformia (lnsecta, Coleoptera), unter besonderer Berücksichtigung der Chrysomelidae
    • Wachmann, E. (1977) Vergleichende Analyse der feinstrukturellen Organisation offener Rhabdome in den Augen der Cucujiformia (lnsecta, Coleoptera), unter besonderer Berücksichtigung der Chrysomelidae. Zoomorphology, 88, 95-131.
    • (1977) Zoomorphology , vol.88 , pp. 95-131
    • Wachmann, E.1
  • 103
    • 0043123111 scopus 로고    scopus 로고
    • RevTrans: multiple alignment of coding DNA from aligned amino acid sequences
    • Wernersson, R. & Pedersen, A.G. (2003) RevTrans: multiple alignment of coding DNA from aligned amino acid sequences. Nucleic Acids Research, 31, 3537-3539.
    • (2003) Nucleic Acids Research , vol.31 , pp. 3537-3539
    • Wernersson, R.1    Pedersen, A.G.2
  • 104
    • 0027083319 scopus 로고
    • Animal mitochondrial DNA: Structure and evolution
    • Wolstenhome, D.R. (1992) Animal mitochondrial DNA: Structure and evolution. International Review of Cytology, 141, 173-216.
    • (1992) International Review of Cytology , vol.141 , pp. 173-216
    • Wolstenhome, D.R.1
  • 105
    • 3943113025 scopus 로고    scopus 로고
    • Use of a PCRbased approach for sequencing whole mitochondrial genomes of insects: two examples (cockroach and dragonfly) based on the method developed for decapod crustaceans
    • Yamauchi, M.M., Miya, M.U. & Nishida, M. (2004) Use of a PCRbased approach for sequencing whole mitochondrial genomes of insects: two examples (cockroach and dragonfly) based on the method developed for decapod crustaceans. Insect Molecular Biology, 13, 435-442.
    • (2004) Insect Molecular Biology , vol.13 , pp. 435-442
    • Yamauchi, M.M.1    Miya, M.U.2    Nishida, M.3
  • 106
    • 0030451420 scopus 로고    scopus 로고
    • Among-site rate variation and its impact on phylogenetic analyses
    • Yang, Z. (1996) Among-site rate variation and its impact on phylogenetic analyses. Trends in Ecology and Evolution, 11, 367-372.
    • (1996) Trends in Ecology and Evolution , vol.11 , pp. 367-372
    • Yang, Z.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.