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Volumn 24, Issue 8, 2007, Pages 1667-1677

Population genetics without intraspecific data

Author keywords

Dependence among sites; Fixation probability; Protein structure; RNA structure

Indexed keywords

RNA;

EID: 34547728173     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msm085     Document Type: Article
Times cited : (34)

References (48)
  • 1
    • 14544283723 scopus 로고    scopus 로고
    • Root of the Eukaryota tree as inferred from combined maximum likelihood analyses of multiple molecular sequence data
    • Arisue N, Hasegawa M, Hashimoto T. 2005. Root of the Eukaryota tree as inferred from combined maximum likelihood analyses of multiple molecular sequence data. Mol Biol Evol. 22:409-420.
    • (2005) Mol Biol Evol , vol.22 , pp. 409-420
    • Arisue, N.1    Hasegawa, M.2    Hashimoto, T.3
  • 2
    • 33748925566 scopus 로고    scopus 로고
    • A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank
    • Bastolla U, Porto M, Roman HE, Vendrulscolo M. 2006. A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank. BMC Evol Biol. 6:43.
    • (2006) BMC Evol Biol , vol.6 , pp. 43
    • Bastolla, U.1    Porto, M.2    Roman, H.E.3    Vendrulscolo, M.4
  • 3
    • 33845503073 scopus 로고    scopus 로고
    • Adaptive evolution of transcription factor binding sites
    • Berg J, Willmann S, Lässig M. 2004. Adaptive evolution of transcription factor binding sites. BMC Evol Biol. 4:42.
    • (2004) BMC Evol Biol , vol.4 , pp. 42
    • Berg, J.1    Willmann, S.2    Lässig, M.3
  • 5
    • 0003218786 scopus 로고
    • A model of evolutionary change in proteins
    • Dayhoff MO, Eck RV, editors, National Biomedical Research Foundation: Washington D.C. p, 68
    • Dayhoff MO, Eck RV. 1968. A model of evolutionary change in proteins. In: Dayhoff MO, Eck RV, editors. Atlas of protein sequence and structure. National Biomedical Research Foundation: Washington D.C. p. 33-41 1967-68.
    • (1967) Atlas of protein sequence and structure , pp. 33-41
    • Dayhoff, M.O.1    Eck, R.V.2
  • 7
    • 33745347447 scopus 로고    scopus 로고
    • The distribution of fitness effects of new deleterious amino acid mutations in humans
    • Eyre-Walker A, Woolfit M, Phelps T. 2006. The distribution of fitness effects of new deleterious amino acid mutations in humans. Genetics. 173:891-900.
    • (2006) Genetics , vol.173 , pp. 891-900
    • Eyre-Walker, A.1    Woolfit, M.2    Phelps, T.3
  • 9
    • 0036083696 scopus 로고    scopus 로고
    • Annexins: From structure to function
    • Gerke V, Moss SE. 2002. Annexins: From structure to function. Physiol Rev. 82:331-371.
    • (2002) Physiol Rev , vol.82 , pp. 331-371
    • Gerke, V.1    Moss, S.E.2
  • 10
    • 0031875569 scopus 로고    scopus 로고
    • Evolutionary distances for protein-coding sequences: Modeling site-specific residue frequencies
    • Halpern AL, Bruno WJ. 1998. Evolutionary distances for protein-coding sequences: Modeling site-specific residue frequencies. Mol Biol Evol. 15:910-917.
    • (1998) Mol Biol Evol , vol.15 , pp. 910-917
    • Halpern, A.L.1    Bruno, W.J.2
  • 11
    • 4243559860 scopus 로고    scopus 로고
    • Compensatory neutral mutations and the evolution of RNA
    • Higgs PG. 1998. Compensatory neutral mutations and the evolution of RNA. Genetica. 102/103: 91-101.
    • (1998) Genetica , vol.102-103 , pp. 91-101
    • Higgs, P.G.1
  • 12
    • 0034522921 scopus 로고    scopus 로고
    • RNA secondary structure: Physical and computational aspects
    • Higgs PG. 2000. RNA secondary structure: Physical and computational aspects. Quart Rev Biophys. 33:199-253.
    • (2000) Quart Rev Biophys , vol.33 , pp. 199-253
    • Higgs, P.G.1
  • 13
    • 84956958332 scopus 로고    scopus 로고
    • Identification of conflicting selective effects on highly expressed genes
    • Higgs PG, Hao WQ, Golding GB. 2007. Identification of conflicting selective effects on highly expressed genes. Evol Bioinf. 2:1-13.
    • (2007) Evol Bioinf , vol.2 , pp. 1-13
    • Higgs, P.G.1    Hao, W.Q.2    Golding, G.B.3
  • 14
  • 16
    • 4644300141 scopus 로고    scopus 로고
    • Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
    • Hwang DG, Green P. 2004. Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc Natl Acad Sci USA. 101:13994-14001.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 13994-14001
    • Hwang, D.G.1    Green, P.2
  • 17
    • 0033537993 scopus 로고    scopus 로고
    • GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
    • Jones DT. 1999. GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol. 287:797-815.
    • (1999) J Mol Biol , vol.287 , pp. 797-815
    • Jones, D.T.1
  • 18
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones DT, Taylor WR, Thornton JM. 1992. A new approach to protein fold recognition. Nature. 358:86-89.
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 19
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • Munro HN, editor, New York: Academic Press. p
    • Jukes TH, Cantor CR. 1969. Evolution of protein molecules. In: Munro HN, editor. Mammalian Protein Metabolism. New York: Academic Press. p. 21-132.
    • (1969) Mammalian Protein Metabolism , pp. 21-132
    • Jukes, T.H.1    Cantor, C.R.2
  • 20
    • 0000800333 scopus 로고
    • On the probability of fixation of mutant genes in a population
    • Kimura M. 1962. On the probability of fixation of mutant genes in a population. Genetics. 47:713-719.
    • (1962) Genetics , vol.47 , pp. 713-719
    • Kimura, M.1
  • 21
    • 0035103260 scopus 로고    scopus 로고
    • Performance of a divergence time estimation method under a probabilistic model of rate evolution
    • Kishino H, Thorne JL, Bruno WJ. 2001. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol Biol Evol. 18:352-361.
    • (2001) Mol Biol Evol , vol.18 , pp. 352-361
    • Kishino, H.1    Thorne, J.L.2    Bruno, W.J.3
  • 22
    • 17444417142 scopus 로고    scopus 로고
    • Using equilibrium frequencies in models of sequence evolution
    • Knudsen B, Miyamoto MM. 2005. Using equilibrium frequencies in models of sequence evolution. BMC Evol Biol. 5:21.
    • (2005) BMC Evol Biol , vol.5 , pp. 21
    • Knudsen, B.1    Miyamoto, M.M.2
  • 23
    • 0033026624 scopus 로고    scopus 로고
    • Using physicalchemistry based mutation models in phylogenetic analyses of HIV-1 subtypes
    • Koshi JM, Mindell DP, Goldstein RA. 1999. Using physicalchemistry based mutation models in phylogenetic analyses of HIV-1 subtypes. Mol Biol Evol. 16:173-179.
    • (1999) Mol Biol Evol , vol.16 , pp. 173-179
    • Koshi, J.M.1    Mindell, D.P.2    Goldstein, R.A.3
  • 24
    • 33644826560 scopus 로고    scopus 로고
    • Computing Bayes factors using thermodynamic integration
    • Lartillot N, Philippe H. 2006. Computing Bayes factors using thermodynamic integration. Syst Biol. 55:195-207.
    • (2006) Syst Biol , vol.55 , pp. 195-207
    • Lartillot, N.1    Philippe, H.2
  • 25
    • 27644482258 scopus 로고    scopus 로고
    • Evolutionary population genetics of promoters: Predicting binding sites and functional phylogenies
    • Mustonen V, Lässig M. 2005. Evolutionary population genetics of promoters: Predicting binding sites and functional phylogenies. Proc Nat Acad Sci USA. 102:15936-15941.
    • (2005) Proc Nat Acad Sci USA , vol.102 , pp. 15936-15941
    • Mustonen, V.1    Lässig, M.2
  • 26
    • 0031972161 scopus 로고    scopus 로고
    • Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    • Nielsen R, Yang Z. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics. 148:929-936.
    • (1998) Genetics , vol.148 , pp. 929-936
    • Nielsen, R.1    Yang, Z.2
  • 27
    • 0042354654 scopus 로고    scopus 로고
    • Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA
    • Nielsen R, Yang Z. 2003. Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. Mol Biol Evol. 20:1231-1239.
    • (2003) Mol Biol Evol , vol.20 , pp. 1231-1239
    • Nielsen, R.1    Yang, Z.2
  • 28
    • 0012088802 scopus 로고
    • Population size and rate of evolution
    • Ohta T. 1972. Population size and rate of evolution. J Mol Evol. 1:305-314.
    • (1972) J Mol Evol , vol.1 , pp. 305-314
    • Ohta, T.1
  • 29
    • 0023477438 scopus 로고
    • Very slightly deleterious mutations and the molecular clock
    • Ohta T. 1987. Very slightly deleterious mutations and the molecular clock. J Mol Evol. 26:1-6.
    • (1987) J Mol Evol , vol.26 , pp. 1-6
    • Ohta, T.1
  • 30
    • 0025173452 scopus 로고
    • Theoretical study of near neutrality. I. Heterozygosity and rate of mutant substitution
    • Ohta T, Tachida H. 1990. Theoretical study of near neutrality. I. Heterozygosity and rate of mutant substitution. Genetics. 126:219-229.
    • (1990) Genetics , vol.126 , pp. 219-229
    • Ohta, T.1    Tachida, H.2
  • 31
    • 0041836283 scopus 로고    scopus 로고
    • Estimating the distribution of fitness effects from DNA sequence data: Implications for the molecular clock
    • Piganeau G, Eyre-Walker A. 2003. Estimating the distribution of fitness effects from DNA sequence data: Implications for the molecular clock. Proc Natl Acad Sci USA. 100:10335-10340.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 10335-10340
    • Piganeau, G.1    Eyre-Walker, A.2
  • 32
    • 28444445926 scopus 로고    scopus 로고
    • R Development Core Team, R Foundation for Statistical Computing, Vienna
    • R Development Core Team. 2006. R: A language and environment for statistical computing. (R Foundation for Statistical Computing, Vienna, 2005). (http://www.R-project.org).
    • (2005) R: A language and environment for statistical computing
  • 33
    • 1542642309 scopus 로고    scopus 로고
    • Protein evolution with dependence among codons due to tertiary structure
    • Robinson DM, Jones D, Kishino H, Goldman N, Thorne JL. 2003. Protein evolution with dependence among codons due to tertiary structure. Mol Biol Evol. 20:1692-1704.
    • (2003) Mol Biol Evol , vol.20 , pp. 1692-1704
    • Robinson, D.M.1    Jones, D.2    Kishino, H.3    Goldman, N.4    Thorne, J.L.5
  • 34
    • 15544374861 scopus 로고    scopus 로고
    • Site interdependence attributed to tertiary structure in amino acid sequence evolution
    • Rodrigue N, Lartillot N, Bryant D, Philippe H. 2005. Site interdependence attributed to tertiary structure in amino acid sequence evolution. Gene. 347:207-217.
    • (2005) Gene , vol.347 , pp. 207-217
    • Rodrigue, N.1    Lartillot, N.2    Bryant, D.3    Philippe, H.4
  • 35
    • 33748126145 scopus 로고    scopus 로고
    • Assessing siteinterdependent phylogenetic models of sequence evolution
    • Rodrigue N, Lartillot N, Philippe H. 2006. Assessing siteinterdependent phylogenetic models of sequence evolution. Mol Biol Evol. 23:1762-1775.
    • (2006) Mol Biol Evol , vol.23 , pp. 1762-1775
    • Rodrigue, N.1    Lartillot, N.2    Philippe, H.3
  • 36
    • 0036135468 scopus 로고    scopus 로고
    • Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach
    • Sanderson MJ. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol Biol Evol. 19:101-109.
    • (2002) Mol Biol Evol , vol.19 , pp. 101-109
    • Sanderson, M.J.1
  • 37
    • 0035156561 scopus 로고    scopus 로고
    • RNA sequence evolution with secondary structure constraints: Comparison of substitution rate models using maximum likelihood methods
    • Savill NJ, Hoyle DC, Higgs PG. 2001. RNA sequence evolution with secondary structure constraints: Comparison of substitution rate models using maximum likelihood methods. Genetics. 157:399-411.
    • (2001) Genetics , vol.157 , pp. 399-411
    • Savill, N.J.1    Hoyle, D.C.2    Higgs, P.G.3
  • 38
    • 22144437325 scopus 로고    scopus 로고
    • The application of statistical physics to evolutionary biology
    • Sella G, Hirsh AE. 2005. The application of statistical physics to evolutionary biology. Proc Natl Acad Sci USA. 102:9541-9546.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 9541-9546
    • Sella, G.1    Hirsh, A.E.2
  • 39
    • 1542510106 scopus 로고    scopus 로고
    • Phylogenetic estimation of contextdependent substitution rates by maximum likelihood
    • Siepel A, Haussler D. 2004. Phylogenetic estimation of contextdependent substitution rates by maximum likelihood. Mol Biol Evol. 21:468-488.
    • (2004) Mol Biol Evol , vol.21 , pp. 468-488
    • Siepel, A.1    Haussler, D.2
  • 42
    • 0031894830 scopus 로고    scopus 로고
    • High apparent rate of simultaneous compensatory basepair substitutions in ribosomal
    • Tillier ERM, Collins RA. 1998. High apparent rate of simultaneous compensatory basepair substitutions in ribosomal RNA. Genetics. 148:1993-2002.
    • (1998) RNA. Genetics , vol.148 , pp. 1993-2002
    • Tillier, E.R.M.1    Collins, R.A.2
  • 43
    • 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
  • 44
    • 27744541698 scopus 로고    scopus 로고
    • Distribution of the strength of selection against amino acid replacements in human proteins
    • Yampolsky LY, Kondrashov FA, Kondrashov AS. 2005. Distribution of the strength of selection against amino acid replacements in human proteins. Hum Mol Genet. 14:3191-3201.
    • (2005) Hum Mol Genet , vol.14 , pp. 3191-3201
    • Yampolsky, L.Y.1    Kondrashov, F.A.2    Kondrashov, A.S.3
  • 45
    • 0034097381 scopus 로고    scopus 로고
    • Codonsubstitution models for variable selection pressure at amino acid sites
    • Yang Z, Nielsen R, Goldman N, Pedersen A-MK. 2000. Codonsubstitution models for variable 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.K.4
  • 46
    • 33748080427 scopus 로고    scopus 로고
    • Dependence among sites in RNA evolution
    • Yu J, Thorne JL. 2006. Dependence among sites in RNA evolution. Mol Biol Evol. 23:1525-1537.
    • (2006) Mol Biol Evol , vol.23 , pp. 1525-1537
    • Yu, J.1    Thorne, J.L.2
  • 47
    • 0024477261 scopus 로고
    • On finding all suboptimal foldings of an RNA molecule
    • Zuker M. 1989. On finding all suboptimal foldings of an RNA molecule. Science. 244:48-52.
    • (1989) Science , vol.244 , pp. 48-52
    • Zuker, M.1
  • 48
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • Zuker M, Stiegler P. 1981. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9:133-148.
    • (1981) Nucleic Acids Res , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2


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