메뉴 건너뛰기




Volumn 7, Issue 11, 2012, Pages

Resolving Discrepancy between Nucleotides and Amino Acids in Deep-Level Arthropod Phylogenomics: Differentiating Serine Codons in 21-Amino-Acid Models

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; AMINO ACID DERIVATIVE; ASPARAGINE; CYSTEINE; GLYCINE; NUCLEOTIDE DERIVATIVE; SERINE; THREONINE; TYROSINE;

EID: 84869805937     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0047450     Document Type: Article
Times cited : (91)

References (31)
  • 2
    • 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 KF, Voss RS, Jansa SA, (2007) Base-compositional heterogeneity in the RAG1 locus among didelphid marsupials: Implications for phylogenetic inference and the evolution of GC content. Syst Biol 56: 83-96.
    • (2007) Syst Biol , vol.56 , pp. 83-96
    • Gruber, K.F.1    Voss, R.S.2    Jansa, S.A.3
  • 3
    • 78649873812 scopus 로고    scopus 로고
    • When phylogenetic assumptions are violated: Base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics
    • Song H, Sheffield NC, Cameron SL, Miller KB, Whiting MF, (2010) When phylogenetic assumptions are violated: Base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics. Syst Ent 39: 429-448.
    • (2010) Syst Ent , vol.39 , pp. 429-448
    • Song, H.1    Sheffield, N.C.2    Cameron, S.L.3    Miller, K.B.4    Whiting, M.F.5
  • 4
    • 79961144454 scopus 로고    scopus 로고
    • Sources of signal in 62 protein-coding nuclear genes for higher-level phylogenetics of arthropods
    • Regier JC, Zwick A, (2011) Sources of signal in 62 protein-coding nuclear genes for higher-level phylogenetics of arthropods. PLoS ONE 6: e23408.
    • (2011) PLoS ONE , vol.6
    • Regier, J.C.1    Zwick, A.2
  • 5
    • 77649189590 scopus 로고    scopus 로고
    • Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences
    • Regier JC, Shultz JW, Zwick A, Hussey A, Ball B, et al. (2010) Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 463: 1079-1083.
    • (2010) Nature , vol.463 , pp. 1079-1083
    • Regier, J.C.1    Shultz, J.W.2    Zwick, A.3    Hussey, A.4    Ball, B.5
  • 6
    • 58149236596 scopus 로고    scopus 로고
    • Resolving arthropod phylogeny: Exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence
    • Regier JC, Shultz JW, Ganley ARD, Hussey A, Shi D, et al. (2008) Resolving arthropod phylogeny: Exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence. Syst Biol 57: 920-938.
    • (2008) Syst Biol , vol.57 , pp. 920-938
    • Regier, J.C.1    Shultz, J.W.2    Ganley, A.R.D.3    Hussey, A.4    Shi, D.5
  • 7
    • 42149157760 scopus 로고    scopus 로고
    • Broad phylogenomic sampling improves resolution of the animal tree of life
    • Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, et al. (2008) Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452: 745-750.
    • (2008) Nature , vol.452 , pp. 745-750
    • Dunn, C.W.1    Hejnol, A.2    Matus, D.Q.3    Pang, K.4    Browne, W.E.5
  • 11
    • 78650474944 scopus 로고    scopus 로고
    • A congruent solution to arthropod phylogeny: Phylogenomics, microRNAs and morphology support monophyletic Mandibulata
    • Rota-Stabelli O, Campbell L, Brinkmann H, Edgecombe GD, Longhorn SJ, et al. (2011) A congruent solution to arthropod phylogeny: Phylogenomics, microRNAs and morphology support monophyletic Mandibulata. Proc Biol Sci 278: 298-306.
    • (2011) Proc Biol Sci , vol.278 , pp. 298-306
    • Rota-Stabelli, O.1    Campbell, L.2    Brinkmann, H.3    Edgecombe, G.D.4    Longhorn, S.J.5
  • 12
    • 0026691182 scopus 로고
    • The rapid generation of mutation matrices from protein sequences
    • Jones DT, Taylor WR, Thornton JM, (1992) The rapid generation of mutation matrices from protein sequences. Comput Appl Biosci 8: 275-282.
    • (1992) Comput Appl Biosci , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 13
    • 0034007922 scopus 로고    scopus 로고
    • Gastropod evolutionary rates and phylogenetic relationships assessed using partial 23S rDNA and histone H3 sequences
    • Colgan DJ, Ponder WF, Eggler PE, (2000) Gastropod evolutionary rates and phylogenetic relationships assessed using partial 23S rDNA and histone H3 sequences. Zoologica Scripta 29: 29-63.
    • (2000) Zoologica Scripta , vol.29 , pp. 29-63
    • Colgan, D.J.1    Ponder, W.F.2    Eggler, P.E.3
  • 14
    • 4644327551 scopus 로고    scopus 로고
    • Phylogenetic artifacts can be caused by leucine, serine, and arginine codon usage heterogeneity: Dinoflagellate plastid origins as a case study
    • Inagaki Y, Simpson AGB, Dacks JB, Roger AJ, (2004) Phylogenetic artifacts can be caused by leucine, serine, and arginine codon usage heterogeneity: Dinoflagellate plastid origins as a case study. Syst Biol 53: 582-593.
    • (2004) Syst Biol , vol.53 , pp. 582-593
    • Inagaki, Y.1    Simpson, A.G.B.2    Dacks, J.B.3    Roger, A.J.4
  • 15
    • 0034681511 scopus 로고    scopus 로고
    • Evidence for a high frequency of simultaneous double-nucleotide substitutions
    • Averof M, Rokas A, Wolfe KH, Sharp PM, (2000) Evidence for a high frequency of simultaneous double-nucleotide substitutions. Science 287: 1283-1286.
    • (2000) Science , vol.287 , pp. 1283-1286
    • Averof, M.1    Rokas, A.2    Wolfe, K.H.3    Sharp, P.M.4
  • 17
    • 34547675965 scopus 로고    scopus 로고
    • An empirical codon model for protein sequence evolution
    • Kosiol C, Holmes I, Goldman N, (2007) An empirical codon model for protein sequence evolution. Mol Biol Evol 24: 1464-1479.
    • (2007) Mol Biol Evol , vol.24 , pp. 1464-1479
    • Kosiol, C.1    Holmes, I.2    Goldman, N.3
  • 19
    • 55049083550 scopus 로고    scopus 로고
    • The chelifores of sea spiders (Arthropoda, Pycnogonida) are the appendages of the deutocerebral segment
    • Brenneis G, Ungerer P, Scholtz G, (2008) The chelifores of sea spiders (Arthropoda, Pycnogonida) are the appendages of the deutocerebral segment. Evolution & Development 10: 717-724.
    • (2008) Evolution & Development , vol.10 , pp. 717-724
    • Brenneis, G.1    Ungerer, P.2    Scholtz, G.3
  • 20
    • 9744246914 scopus 로고    scopus 로고
    • Phylogenetic analysis of Myriapoda using three nuclear protein-coding genes
    • Regier JC, Wilson HM, Shultz JW, (2005) Phylogenetic analysis of Myriapoda using three nuclear protein-coding genes. Mol Evol Phylogen 34: 147-158.
    • (2005) Mol Evol Phylogen , vol.34 , pp. 147-158
    • Regier, J.C.1    Wilson, H.M.2    Shultz, J.W.3
  • 21
    • 34147157163 scopus 로고    scopus 로고
    • Myriapod monophyly and relationships among myriapod classes based on nearly complete 28S and 18S rDNA sequences
    • Gai Y-H, Song DX, Sun H-Y, Zhou K-Y, (2006) Myriapod monophyly and relationships among myriapod classes based on nearly complete 28S and 18S rDNA sequences. Zool Sci 23: 1101-1108.
    • (2006) Zool Sci , vol.23 , pp. 1101-1108
    • Gai, Y.-H.1    Song, D.X.2    Sun, H.-Y.3    Zhou, K.-Y.4
  • 22
    • 31344433677 scopus 로고    scopus 로고
    • An empirical examination of the utility of codon-substitution models in phylogeny reconstruction
    • Ren F, Tanaka H, Yang Z, (2005) An empirical examination of the utility of codon-substitution models in phylogeny reconstruction. Syst Biol 54: 808-818.
    • (2005) Syst Biol , vol.54 , pp. 808-818
    • Ren, F.1    Tanaka, H.2    Yang, Z.3
  • 23
    • 67749114398 scopus 로고    scopus 로고
    • Statistical comparison of nucleotide, amino acid, and codon substitution models for evolutionary analysis of protein-coding sequences
    • Seo T-K, Kishino H, (2009) Statistical comparison of nucleotide, amino acid, and codon substitution models for evolutionary analysis of protein-coding sequences. Syst Biol 58: 199-210.
    • (2009) Syst Biol , vol.58 , pp. 199-210
    • Seo, T.-K.1    Kishino, H.2
  • 24
    • 0037058983 scopus 로고    scopus 로고
    • Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics
    • Suzuki Y, Glazko GV, Nei M, (2002) Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc Natl Acad Sci USA 99: 16138-16143.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 16138-16143
    • Suzuki, Y.1    Glazko, G.V.2    Nei, M.3
  • 25
    • 35748943561 scopus 로고    scopus 로고
    • On reduced amino acid alphabets for phylogenetic inference
    • Susko E, Roger AJ, (2007) On reduced amino acid alphabets for phylogenetic inference. Mol Biol Evol 24: 2139-2150.
    • (2007) Mol Biol Evol , vol.24 , pp. 2139-2150
    • Susko, E.1    Roger, A.J.2
  • 26
    • 0041385962 scopus 로고    scopus 로고
    • Pandit: a database of protein and associated nucleotide domains with inferred trees
    • Whelan S, de Bakker P, Goldman N, (2003) Pandit: a database of protein and associated nucleotide domains with inferred trees. Bioinformatics 19: 1556-1563.
    • (2003) Bioinformatics , vol.19 , pp. 1556-1563
    • Whelan, S.1    de Bakker, P.2    Goldman, N.3
  • 27
    • 33644878388 scopus 로고    scopus 로고
    • PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees
    • Whelan S, de Bakker P, Quevillon E, Rodriguez N, Goldman N, (2006) PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. Nucleic Acids Research 34: D327-D331.
    • (2006) Nucleic Acids Research , vol.34
    • Whelan, S.1    de Bakker, P.2    Quevillon, E.3    Rodriguez, N.4    Goldman, N.5
  • 28
    • 84971562539 scopus 로고    scopus 로고
    • MacClade 4: Analysis of phylogeny and character evolution
    • Maddison WP, Maddison DR, (2002) MacClade 4: Analysis of phylogeny and character evolution. Sinauer Associates.
    • (2002) Sinauer Associates
    • Maddison, W.P.1    Maddison, D.R.2
  • 30
    • 7444248604 scopus 로고    scopus 로고
    • PAUP*: Phylogenetic analysis using parsimony (* and other methods), version 4.0b 10
    • Swofford DL, (2003) PAUP*: Phylogenetic analysis using parsimony (* and other methods), version 4.0b 10. Sinauer Associates.
    • (2003) Sinauer Associates
    • Swofford, D.L.1
  • 31
    • 72949090454 scopus 로고    scopus 로고
    • The Lattice Project: A Grid research and production environment combining multiple Grid computing models
    • Weber, M.H.W. (Ed.), Principles, Applications and Supporting Communities, Tectum Publishing, Marburg
    • Bazinet AL, Cummings MP (2009) The Lattice Project: A Grid research and production environment combining multiple Grid computing models. In Weber, M.H.W. (Ed.) Distributed & Grid Computing - Science Made Transparent for Everyone. Principles, Applications and Supporting Communities. Pages 2-13. Tectum Publishing, Marburg.
    • (2009) Distributed & Grid Computing - Science Made Transparent for Everyone , pp. 2-13
    • Bazinet, A.L.1    Cummings, M.P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.