메뉴 건너뛰기




Volumn 24, Issue 2, 2007, Pages 513-521

Variation in evolutionary processes at different codon positions

Author keywords

Adaptive evolution; Codon positions; Phylogenetic inference; Protein coding sequences; Sequence evolution

Indexed keywords

ARTICLE; CODON; DATA BASE; DNA SEQUENCE; GENE MUTATION; GENETIC CODE; GENETIC VARIABILITY; MOLECULAR EVOLUTION; PROTEIN FUNCTION;

EID: 33846799228     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msl178     Document Type: Article
Times cited : (87)

References (36)
  • 1
    • 0029974748 scopus 로고    scopus 로고
    • Model of amino acid substitution in proteins encoded by mitochondrial DNA
    • Adachi J, Waddell PJ, Martin W, Hasegawa, M. 2000. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J Mol Evol. 42:459-468.
    • (2000) J Mol Evol , vol.42 , pp. 459-468
    • Adachi, J.1    Waddell, P.J.2    Martin, W.3    Hasegawa, M.4
  • 2
    • 12344283074 scopus 로고    scopus 로고
    • Determinants of adaptive evolution at the molecular level: The extended complexity hypothesis
    • Aris-Brosou S. 2005. Determinants of adaptive evolution at the molecular level: the extended complexity hypothesis. Mol Biol Evol. 22:200-209.
    • (2005) Mol Biol Evol , vol.22 , pp. 200-209
    • Aris-Brosou, S.1
  • 5
    • 0031662136 scopus 로고    scopus 로고
    • The genetic code is one in a million
    • Freeland S, Hurst L. 1998. The genetic code is one in a million. J Mol Evol. 47:238-248.
    • (1998) J Mol Evol , vol.47 , pp. 238-248
    • Freeland, S.1    Hurst, L.2
  • 7
    • 0020383449 scopus 로고
    • Estimation of average number of nucleotide substitutions when the rate of substitution varies with nucleotide
    • Gojobori T, Ishii K, Nei M. 1982. Estimation of average number of nucleotide substitutions when the rate of substitution varies with nucleotide. J Mol Evol. 18:414-422.
    • (1982) J Mol Evol , vol.18 , pp. 414-422
    • Gojobori, T.1    Ishii, K.2    Nei, M.3
  • 8
    • 0027423317 scopus 로고
    • Statistical tests of models of DNA substitution
    • Goldman N. 1993. Statistical tests of models of DNA substitution. J Mol Evol. 37:650-661.
    • (1993) J Mol Evol , vol.37 , pp. 650-661
    • Goldman, N.1
  • 9
    • 0028168856 scopus 로고
    • A codon-based model of nucleotide substitution for protein-coding DNA sequences
    • Goldman N, Yang Z. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol. 11:725-736.
    • (1994) Mol Biol Evol , vol.11 , pp. 725-736
    • Goldman, N.1    Yang, Z.2
  • 10
    • 0022376704 scopus 로고
    • Dating the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa M, Kishino H, Yano T. 1985. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 22:160-174.
    • (1985) J Mol Evol , vol.22 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 11
    • 0032923454 scopus 로고    scopus 로고
    • Variation in the pattern of nucleotide substitution across sites
    • Huelsenbeck J, Nielsen R. 1999. Variation in the pattern of nucleotide substitution across sites. J Mol Evol. 48:86-93.
    • (1999) J Mol Evol , vol.48 , pp. 86-93
    • Huelsenbeck, J.1    Nielsen, R.2
  • 12
    • 0029960344 scopus 로고    scopus 로고
    • Patterns of nucleotide substitution in mitochondrial protein coding genes of vertebrates
    • Kumar S. 1996. Patterns of nucleotide substitution in mitochondrial protein coding genes of vertebrates. Genetics. 143:537-548.
    • (1996) Genetics , vol.143 , pp. 537-548
    • Kumar, S.1
  • 13
    • 4444311171 scopus 로고    scopus 로고
    • Multiple-sequence functional annotation and the generalized hidden Markov phylogeny
    • McAuliffe JD, Pachter L, Jordan MI. 2004. Multiple-sequence functional annotation and the generalized hidden Markov phylogeny. Bioinformatics. 20:1850-1860.
    • (2004) Bioinformatics , vol.20 , pp. 1850-1860
    • McAuliffe, J.D.1    Pachter, L.2    Jordan, M.I.3
  • 14
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with applications to the chloroplast genome
    • Muse S, Gaut B. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with applications to the chloroplast genome. Mol Biol Evol. 11:715-724.
    • (1994) Mol Biol Evol , vol.11 , pp. 715-724
    • Muse, S.1    Gaut, B.2
  • 15
    • 0034019771 scopus 로고    scopus 로고
    • Phylogeny of eukaryotes based on ribosomal RNA: Long-branch attraction and models of sequence evolution
    • Philippe H, Germot A. 2000. Phylogeny of eukaryotes based on ribosomal RNA: long-branch attraction and models of sequence evolution. Mol Biol Evol. 17:830-834.
    • (2000) Mol Biol Evol , vol.17 , pp. 830-834
    • Philippe, H.1    Germot, A.2
  • 16
    • 3042550872 scopus 로고    scopus 로고
    • Genome-scale phylogeny and the detection of systematic biases
    • Phillips M, Delsuc F, Penny D. 2004. Genome-scale phylogeny and the detection of systematic biases. Mol Biol Evol. 21:1455-1458.
    • (2004) Mol Biol Evol , vol.21 , pp. 1455-1458
    • Phillips, M.1    Delsuc, F.2    Penny, D.3
  • 17
    • 0031773680 scopus 로고    scopus 로고
    • Modeltest: Testing the model of DNA substitution
    • Posada D, Crandall K. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics. 14:817-818.
    • (1998) Bioinformatics , vol.14 , pp. 817-818
    • Posada, D.1    Crandall, K.2
  • 18
    • 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
  • 19
    • 28944450584 scopus 로고    scopus 로고
    • Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences
    • Shapiro B, Rambaut A, Drummond A. 2006. Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol Biol Evol. 23:7-9.
    • (2006) Mol Biol Evol , vol.23 , pp. 7-9
    • Shapiro, B.1    Rambaut, A.2    Drummond, A.3
  • 20
    • 0029880314 scopus 로고    scopus 로고
    • The effect of topology on estimates of among-site variation
    • Sullivan J, Holsinger K, Simon C. 1996. The effect of topology on estimates of among-site variation. J Mol Evol. 42:308-312.
    • (1996) J Mol Evol , vol.42 , pp. 308-312
    • Sullivan, J.1    Holsinger, K.2    Simon, C.3
  • 21
    • 79959503826 scopus 로고    scopus 로고
    • The international HapMap project
    • The International HapMap Consortium
    • The International HapMap Consortium. 2003. The international HapMap project. Nature. 426:789-796.
    • (2003) Nature , vol.426 , pp. 789-796
  • 22
    • 33644878388 scopus 로고    scopus 로고
    • PANDIT: An evolution-centric database of protein and associated nucleotide domains with inferred trees
    • Whelan S, de Bakker PIW, Quevillon E, Rodriguez N, Goldman N. 2006. PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. Nucleic Acids Res. 34:D327-D331.
    • (2006) Nucleic Acids Res , vol.34
    • Whelan, S.1    de Bakker, P.I.W.2    Quevillon, E.3    Rodriguez, N.4    Goldman, N.5
  • 23
    • 0032843848 scopus 로고    scopus 로고
    • Distributions of statistics used for the comparison of models of sequence evolution in phylogenetics
    • Whelan S, Goldman N. 1999. Distributions of statistics used for the comparison of models of sequence evolution in phylogenetics. Mol Biol Evol. 16:1292-1299.
    • (1999) Mol Biol Evol , vol.16 , pp. 1292-1299
    • Whelan, S.1    Goldman, N.2
  • 24
    • 4644373240 scopus 로고    scopus 로고
    • Estimating the frequency of events that cause multiple-nucleotide changes
    • Whelan S, Goldman N. 2004. Estimating the frequency of events that cause multiple-nucleotide changes. Genetics. 167:2027-2043.
    • (2004) Genetics , vol.167 , pp. 2027-2043
    • Whelan, S.1    Goldman, N.2
  • 25
    • 0035339920 scopus 로고    scopus 로고
    • Molecular phylogenetics: State-of-the-art methods for looking into the past
    • Whelan S, Liò P, Goldman N. 2001. Molecular phylogenetics: state-of-the-art methods for looking into the past. Trends Genet. 17:261-272.
    • (2001) Trends Genet , vol.17 , pp. 261-272
    • Whelan, S.1    Liò, P.2    Goldman, N.3
  • 26
    • 0027132974 scopus 로고
    • Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
    • Yang Z. 1993. Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol. 10:1396-1401.
    • (1993) Mol Biol Evol , vol.10 , pp. 1396-1401
    • Yang, Z.1
  • 27
    • 0028214103 scopus 로고
    • Estimating the pattern of nucleotide substitution
    • Yang Z. 1994a. Estimating the pattern of nucleotide substitution. J Mol Evol. 39:105-111.
    • (1994) J Mol Evol , vol.39 , pp. 105-111
    • Yang, Z.1
  • 28
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • Yang Z. 1994b. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol. 39:306-314.
    • (1994) J Mol Evol , vol.39 , pp. 306-314
    • Yang, Z.1
  • 29
    • 0029970097 scopus 로고    scopus 로고
    • Maximum-likelihood models for combined analyses of multiple sequence data
    • Yang Z. 1996. Maximum-likelihood models for combined analyses of multiple sequence data. J Mol Evol. 42:587-596.
    • (1996) J Mol Evol , vol.42 , pp. 587-596
    • Yang, Z.1
  • 30
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 13:555-556.
    • (1997) Comput Appl Biosci , vol.13 , pp. 555-556
    • Yang, Z.1
  • 31
    • 0033639150 scopus 로고    scopus 로고
    • Statistical methods for detecting molecular adaptation
    • Yang Z, Bielawski JP. 2000. Statistical methods for detecting molecular adaptation. Trends Ecol Evol. 15:496-503.
    • (2000) Trends Ecol Evol , vol.15 , pp. 496-503
    • Yang, Z.1    Bielawski, J.P.2
  • 32
    • 0028267146 scopus 로고
    • Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation
    • Yang Z, Goldman N, Friday A. 1994. Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol Biol Evol. 11:316-324.
    • (1994) Mol Biol Evol , vol.11 , pp. 316-324
    • Yang, Z.1    Goldman, N.2    Friday, A.3
  • 33
    • 0029469716 scopus 로고
    • Maximum likelihood trees from DNA sequences: A peculiar statistical estimation problem
    • Yang Z, Goldman N, Friday A. 1995. Maximum likelihood trees from DNA sequences: a peculiar statistical estimation problem. Syst Biol. 44:384-399.
    • (1995) Syst Biol , vol.44 , pp. 384-399
    • Yang, Z.1    Goldman, N.2    Friday, A.3
  • 34
    • 0028805929 scopus 로고
    • Molecular evolution of the hepatitis B virus genome
    • Yang Z, Lauder IJ, Lin HJ. 1995. Molecular evolution of the hepatitis B virus genome. J Mol Evol. 41:587-596.
    • (1995) J Mol Evol , vol.41 , pp. 587-596
    • Yang, Z.1    Lauder, I.J.2    Lin, H.J.3
  • 35
    • 0034097381 scopus 로고    scopus 로고
    • Codon-substitution models for the heterogeneous selection pressure at amino acid sites
    • Yang Z, Nielsen R, Goldman N, Pedersen A-M. 2000. Codon-substitution models for the heterogeneous selection pressure at amino acid sites. Genetics. 155:431-449.
    • (2000) Genetics , vol.155 , pp. 431-449
    • Yang, Z.1    Nielsen, R.2    Goldman, N.3    Pedersen, A.-M.4
  • 36
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.