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Volumn 62, Issue 1, 2013, Pages 121-133

Serine codon-usage bias in deep phylogenomics: Pancrustacean relationships as a case study

Author keywords

21 states CAT model; 23 states CAT model; Codon usage bias; nucleotide composition bias; Pancrustacea; phylogenomics; serine

Indexed keywords

AMINO ACID; NUCLEOTIDE 3' PYROPHOSPHOKINASE 2',3' CYCLIC MONOPHOSPHOKINASE; NUCLEOTIDE 3'-PYROPHOSPHOKINASE-2',3'-CYCLIC MONOPHOSPHOKINASE; PHOSPHOTRANSFERASE; SERINE;

EID: 84871849373     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/sys077     Document Type: Article
Times cited : (121)

References (51)
  • 1
    • 1342309210 scopus 로고    scopus 로고
    • Parallel Metropolis-coupledMarkov chain Monte Carlo forBayesian phylogenetic inference
    • Altekar G., Dwarkadas S., Huelsenbeck J. P., Ronquist F. 2004. Parallel Metropolis-coupledMarkov chain Monte Carlo forBayesian phylogenetic inference. Bioinformatics 20:407-415.
    • (2004) Bioinformatics , vol.20 , pp. 407-415
    • Altekar, G.1    Dwarkadas, S.2    Huelsenbeck, J.P.3    Ronquist, F.4
  • 2
    • 0034681511 scopus 로고    scopus 로고
    • Evidence for a high frequency of simultaneous double-nucleotide substitutions
    • Averof M., Rokas A., Wolfe K. H., Sharp P. M. 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
  • 3
    • 47249122561 scopus 로고    scopus 로고
    • A site-and time-heterogeneous model of amino acid replacement
    • Blanquart S., Lartillot N. 2008. A site-and time-heterogeneous model of amino acid replacement. Mol. Biol. Evol. 25:842-858.
    • (2008) Mol. Biol. Evol , vol.25 , pp. 842-858
    • Blanquart, S.1    Lartillot, N.2
  • 4
    • 0033015732 scopus 로고    scopus 로고
    • Archaea sister group of bacteria Indications fromtree reconstruction artifacts in ancient phylogenies
    • Brinkmann H., Phillipe H. 1999. Archaea sister group of bacteria Indications fromtree reconstruction artifacts in ancient phylogenies. Mol. Biol. Evol. 16:817-825.
    • (1999) Mol. Biol. Evol , vol.16 , pp. 817-825
    • Brinkmann, H.1    Phillipe, H.2
  • 6
    • 24044511196 scopus 로고    scopus 로고
    • Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic
    • Cook C. E., Yue Q., Akam M. 2005. Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic. Proc. R. Soc. B 272:1295-1304.
    • (2005) Proc. R. Soc B , vol.272 , pp. 1295-1304
    • Cook, C.E.1    Yue, Q.2    Akam, M.3
  • 7
    • 80051782566 scopus 로고    scopus 로고
    • A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases
    • Cummins C. A., McInerney J. O. 2011. A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases. Syst. Biol. 60(6):833-844.
    • (2011) Syst. Biol. , vol.60 , Issue.6 , pp. 833-844
    • Cummins, C.A.1    McInerney, J.O.2
  • 8
    • 0027265023 scopus 로고
    • Reduced thermophilic bias in the 16S rDNA sequence from Thermus rubber provides further support for a relationship between Thermus and Deinococcus
    • Embley T. M., Thomas R., Williams R. 1993. Reduced thermophilic bias in the 16S rDNA sequence from Thermus rubber provides further support for a relationship between Thermus and Deinococcus. Syst. Appl. Microbiol. 16:25-29.
    • (1993) Syst. Appl. Microbiol , vol.16 , pp. 25-29
    • Embley, T.M.1    Thomas, R.2    Williams, R.3
  • 10
    • 1642290708 scopus 로고    scopus 로고
    • The brain of the Remipedia (Crustacea) and an alternative hypothesis on their phylogenetic relationships
    • Fanenbruck M., Harzsch S., Wägele J. W. 2004. The brain of the Remipedia (Crustacea) and an alternative hypothesis on their phylogenetic relationships. Proc. Natl Acad. Sci. USA 101: 3868-3873.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 3868-3873
    • Fanenbruck, M.1    Harzsch, S.2    Wägele, J.W.3
  • 11
    • 3242701529 scopus 로고    scopus 로고
    • Modeling compositional heterogeneity
    • Foster P. G. 2004. Modeling compositional heterogeneity. Syst. Biol. 53:485-495.
    • (2004) Syst. Biol , vol.53 , pp. 485-495
    • Foster, P.G.1
  • 12
    • 67651039738 scopus 로고    scopus 로고
    • The primary divisions of life: A phylogenomic approach employing composition-heterogeneous methods
    • Foster P. G, Cox C. J., Embley T. M. 2009. The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods. Phil. Trans. R. Soc. B 364:2197-2207.
    • (2009) Phil. Trans. R. Soc B , vol.364 , pp. 2197-2207
    • Foster, P.G.1    Cox, C.J.2    Embley, T.M.3
  • 13
    • 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. J. Mol. Evol. 48:284-290.
    • (1999) J. Mol. Evol , vol.48 , pp. 284-290
    • Foster, P.G.1    Hickey, D.A.2
  • 14
    • 0031020582 scopus 로고    scopus 로고
    • Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria
    • Foster P. G., Jermiin L. S., Hickey D. A. 1997. Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria. J. Mol. Evol. 44:282-288.
    • (1997) J. Mol. Evol , vol.44 , pp. 282-288
    • Foster, P.G.1    Jermiin, L.S.2    Hickey, D.A.3
  • 15
    • 0028790653 scopus 로고
    • Inferring phylogenies from DNA sequences of unequal base compositions
    • Galtier N., Gouy M. 1995. Inferring phylogenies from DNA sequences of unequal base compositions. Proc. Natl Acad. of Sci. USA 92: 11317-11321.
    • (1995) Proc. Natl Acad. of Sci. USA , vol.92 , pp. 11317-11321
    • Galtier, N.1    Gouy, M.2
  • 16
    • 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. Mol. Biol. Evol. 22:251-264.
    • (2005) Mol. Biol. Evol , vol.22 , pp. 251-264
    • Gibson, A.1    Gowri-Shankar, V.2    Higgs, P.G.3    Rattray, M.4
  • 17
    • 57149093199 scopus 로고    scopus 로고
    • Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes
    • Holder M. T., Zwickl D. J., Dessimoz C. 2008. Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes. Phil. Trans. R. Soc. B 363:4013-4021.
    • (2008) Phil. Trans. R. Soc B , vol.363 , pp. 4013-4021
    • Holder, M.T.1    Zwickl, D.J.2    Dessimoz, C.3
  • 18
    • 10344254308 scopus 로고    scopus 로고
    • Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex i
    • Hrdy I., Hirt R. P., Dolezal P., Bardonova L., Foster P. G., Tachezy J., Embley T. M. 2004. Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I. Nature 432:618-622.
    • (2004) Nature , vol.432 , pp. 618-622
    • Hrdy, I.1    Hirt, R.P.2    Dolezal, P.3    Bardonova, L.4    Foster, P.G.5    Tachezy, J.6    Embley, T.M.7
  • 19
    • 33745810231 scopus 로고    scopus 로고
    • Phylogenetic estimation under codon models can be biased by codon usage heterogeneity
    • Inagaki Y., Roger A. J. 2006. Phylogenetic estimation under codon models can be biased by codon usage heterogeneity. Mol. Phylogenet. Evol. 40:428-434.
    • (2006) Mol. Phylogenet. Evol , vol.40 , pp. 428-434
    • Inagaki, Y.1    Roger, A.J.2
  • 20
    • 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 A., Dacks J., Roger A. 2004. Phylogenetic artifacts can be caused by leucine, serine, and arginine codon usage heterogeneity: dinoflagellate plastid origins as a case study. Syst. Biol. 253:582-593.
    • (2004) Syst. Biol , vol.253 , pp. 582-593
    • Inagaki, Y.1    Simpson, A.2    Dacks, J.3    Roger, A.4
  • 22
    • 4644299089 scopus 로고    scopus 로고
    • The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated
    • Jermiin L. S., Ho S. Y. W., Ababneh F., Robinson J., Larkum A. W. D. 2004. The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated. Syst. Biol. 53:638-643.
    • (2004) Syst. Biol , vol.53 , pp. 638-643
    • Jermiin, L.S.1    Ho, S.Y.W.2    Ababneh, F.3    Robinson, J.4    Larkum, A.W.D.5
  • 23
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones D. T., Taylor W. R., Thornton J. M. 1992. The rapid generation of mutation data 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
  • 24
    • 0021277009 scopus 로고
    • A new method for calculating evolutionary substitution rates
    • Lanave C., Preparata G., Saccone C., Serio G. 1984. A new method for calculating evolutionary substitution rates. J. Mol. Evol. 20:86-93.
    • (1984) J. Mol. Evol , vol.20 , pp. 86-93
    • Lanave, C.1    Preparata, G.2    Saccone, C.3    Serio, G.4
  • 25
    • 69949126557 scopus 로고    scopus 로고
    • PhyloBayes 3: A Bayesian software package for phylogenetic reconstruction and molecular dating
    • Lartillot N., Lepage T., Blanquart S. 2009. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25:2286-2288.
    • (2009) Bioinformatics , vol.25 , pp. 2286-2288
    • Lartillot, N.1    Lepage, T.2    Blanquart, S.3
  • 26
    • 2442691520 scopus 로고    scopus 로고
    • ABayesian mixturemodel for across-site heterogeneities in the amino-acid replacement process
    • Lartillot N., Philippe H. 2004. ABayesian mixturemodel for across-site heterogeneities in the amino-acid replacement process. Mol. Biol. Evol. 21:1095-1109.
    • (2004) Mol. Biol. Evol , vol.21 , pp. 1095-1109
    • Lartillot, N.1    Philippe, H.2
  • 27
    • 45849154166 scopus 로고    scopus 로고
    • Animproved general amino acid replacement matrix
    • Le S. Q., Gascuel O. 2008. Animproved general amino acid replacement matrix. Mol. Biol. Evol. 25:1307-1320.
    • (2008) Mol. Biol. Evol , vol.25 , pp. 1307-1320
    • Le, S.Q.1    Gascuel, O.2
  • 28
    • 0026681831 scopus 로고
    • Substitutional bias confounds inference of cyanel origins from sequence data
    • Lockhart P. J., Howe C. J., Bryant D. A., Beanland T. J., Larkum A. W. D. 1992. Substitutional bias confounds inference of cyanel origins from sequence data. J. Mol. Evol. 34:153-162.
    • (1992) J. Mol. Evol , vol.34 , pp. 153-162
    • Lockhart, P.J.1    Howe, C.J.2    Bryant, D.A.3    Beanland, T.J.4    Larkum, A.W.D.5
  • 29
    • 33746693659 scopus 로고    scopus 로고
    • Further use of nearly complete 28S and 18S rRNA genes to classify Ecdysozoa: 37 more arthropods and a kinorhynch
    • Mallatt J., Giribet G. 2006. Further use of nearly complete 28S and 18S rRNA genes to classify Ecdysozoa: 37 more arthropods and a kinorhynch. Mol. Phylogenet. Evol. 40:772-794.
    • (2006) Mol. Phylogenet. Evol , vol.40 , pp. 772-794
    • Mallatt, J.1    Giribet, G.2
  • 30
    • 0031851853 scopus 로고    scopus 로고
    • GCUA: General codon usage analysis
    • McInerney J. O. 1998. GCUA: general codon usage analysis. Bioinformatics 14:372-373.
    • (1998) Bioinformatics , vol.14 , pp. 372-373
    • McInerney, J.O.1
  • 32
    • 0029049426 scopus 로고
    • Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes
    • Perna N. T., Kocher T. D. 1995. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J. Mol. Evol. 41:353-358.
    • (1995) J. Mol. Evol , vol.41 , pp. 353-358
    • Perna, N.T.1    Kocher, T.D.2
  • 34
    • 16844382374 scopus 로고    scopus 로고
    • Pancrustacean phylogeny: Hexapods are terrestrial crustaceans and maxillopods are not monophyletic
    • Regier J. C., Shultz J. W., Kambic R. E. 2005. Pancrustacean phylogeny: hexapods are terrestrial crustaceans and maxillopods are not monophyletic. Proc. R. Soc. B 272:395-401.
    • (2005) Proc. R. Soc B , vol.272 , pp. 395-401
    • Regier, J.C.1    Shultz, J.W.2    Kambic, R.E.3
  • 36
    • 79961144454 scopus 로고    scopus 로고
    • Sources of signal in 62 protein-coding nuclear genes for higher-level phylogenetics of Arthropoda
    • Regier J. C., Zwick A. 2011. Sources of signal in 62 protein-coding nuclear genes for higher-level phylogenetics of Arthropoda. PLoS One 6(8):e23408.
    • (2011) PLoS One , vol.6 , Issue.8
    • Regier, J.C.1    Zwick, A.2
  • 37
    • 77949536563 scopus 로고    scopus 로고
    • Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles
    • Rodrigue N., Philippe H., Lartillot N. 2010. Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles. Proc. Natl Acad. Sci. USA 107:4629-4634.
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 4629-4634
    • Rodrigue, N.1    Philippe, H.2    Lartillot, N.3
  • 39
    • 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
  • 42
    • 67349159068 scopus 로고    scopus 로고
    • MtZoa: A general mitochondrial amino acid substitutions model for animal evolutionary studies
    • Rota-Stabelli O., Yang Z., Telford M. J. 2009. MtZoa: a general mitochondrial amino acid substitutions model for animal evolutionary studies. Mol. Phylogenet. Evol. 52: 268-272.
    • (2009) Mol. Phylogenet. Evol , vol.52 , pp. 268-272
    • Rota-Stabelli, O.1    Yang, Z.2    Telford, M.J.3
  • 43
    • 0032860013 scopus 로고    scopus 로고
    • Evolutionary genomics in Metazoa: The mitochondrial DNA as a model system
    • Saccone C., De Giorgi C., Gissi C., Pesole G., Reyes A. 1999. Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system. Gene 238:195-209.
    • (1999) Gene , vol.238 , pp. 195-209
    • Saccone, C.1    De Giorgi, C.2    Gissi, C.3    Pesole, G.4    Reyes, A.5
  • 44
    • 67749114398 scopus 로고    scopus 로고
    • Statistical comparison of nucleotide, amino acid, and codon substitution models for evolutionary analysis of protein-coding sequences
    • Seo T., 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.1    Kishino, H.2
  • 45
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 46
    • 0000629975 scopus 로고
    • Cross-validatory choice and assessment of statistical predictions
    • Stone M. 1974. Cross-validatory choice and assessment of statistical predictions. J. R. Stat. Soc. B 36:111-147.
    • (1974) J. R. Stat. Soc B , vol.36 , pp. 111-147
    • Stone, M.1
  • 49
    • 0025952777 scopus 로고
    • Archaeal phylogeny: Reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts
    • Woese C. R., Achenbach L., Rouviere P., Mandelco L. 1991. Archaeal phylogeny: reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts. Syst. Appl. Microbiol. 14:364-371.
    • (1991) Syst. Appl. Microbiol , vol.14 , pp. 364-371
    • Woese, C.R.1    Achenbach, L.2    Rouviere, P.3    Mandelco, L.4
  • 50
    • 0031792828 scopus 로고    scopus 로고
    • Models of amino acid substitution and applications to mitochondrial protein evolution
    • Yang Z., Nielsen R., Hasegawa M. 1998. Models of amino acid substitution and applications to mitochondrial protein evolution. Mol. Biol. Evol. 15:1600-1611.
    • (1998) Mol. Biol. Evol , vol.15 , pp. 1600-1611
    • Yang, Z.1    Nielsen, R.2    Hasegawa, M.3
  • 51
    • 0028961933 scopus 로고
    • On the use of nucleic acid sequences to infer early branches in the tree of life
    • Yang Z., Roberts D. 1995. On the use of nucleic acid sequences to infer early branches in the tree of life. Mol. Biol. Evol. 12: 451-458.
    • (1995) Mol. Biol. Evol , vol.12 , pp. 451-458
    • Yang, Z.1    Roberts, D.2


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