메뉴 건너뛰기




Volumn , Issue , 2012, Pages

Codon models as a vehicle for reconciling population genetics with interspecific sequence data

Author keywords

Codon models; Halpern and Bruno; Inter specific data; Mutation selection balance; Population genetic inference

Indexed keywords


EID: 84938520945     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1093/acprof:osobl/9780199601165.003.0007     Document Type: Chapter
Times cited : (11)

References (61)
  • 1
    • 67349233126 scopus 로고    scopus 로고
    • Ancestral processes with selection: Branching and Moran models
    • Baake E, Bialowons R. (2008). Ancestral processes with selection: Branching and Moran models. Banach Center Publ 80: 33-52.
    • (2008) Banach Center Publ , vol.80 , pp. 33-52
    • Baake, E.1    Bialowons, R.2
  • 2
    • 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
  • 3
    • 70350676692 scopus 로고    scopus 로고
    • Fast optimization of statistical potentials for structurally constrained phylogenetic models
    • Bonnard C, Kleinman CL, Rodrigue N, Lartillot N. (2009). Fast optimization of statistical potentials for structurally constrained phylogenetic models. BMC Evol Biol 9: 227.
    • (2009) BMC Evol Biol , vol.9 , pp. 227
    • Bonnard, C.1    Kleinman, C.L.2    Rodrigue, N.3    Lartillot, N.4
  • 4
    • 0029856518 scopus 로고    scopus 로고
    • Modeling residue usage in aligned protein sequences via maximum likelihood
    • Bruno WJ. (1996). Modeling residue usage in aligned protein sequences via maximum likelihood. Mol Biol Evol 13: 1368-1374.
    • (1996) Mol Biol Evol , vol.13 , pp. 1368-1374
    • Bruno, W.J.1
  • 5
    • 79955411242 scopus 로고    scopus 로고
    • History can matter: Non-markovian behavior of ancestral lineages
    • Cartwright RA, Lartillot N, Thorne JL. (2011). History can matter: Non-markovian behavior of ancestral lineages. Sys Biol 60(3): 276-290.
    • (2011) Sys Biol , vol.60 , Issue.3 , pp. 276-290
    • Cartwright, R.A.1    Lartillot, N.2    Thorne, J.L.3
  • 6
    • 0027305597 scopus 로고
    • The effect of deleterious mutations on neutral molecular variation
    • Charlesworth B, Morgan MT, Charlesworth D. (1993). The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289-1303.
    • (1993) Genetics , vol.134 , pp. 1289-1303
    • Charlesworth, B.1    Morgan, M.T.2    Charlesworth, D.3
  • 7
    • 34547809931 scopus 로고    scopus 로고
    • Quantifying the impact of protein tertiary structure on molecular evolution
    • Choi SC, Hobolth A, Robinson DM, Kishino H, Thorne JL. (2007). Quantifying the impact of protein tertiary structure on molecular evolution. Mol Biol Evol 24:1769-1782.
    • (2007) Mol Biol Evol , vol.24 , pp. 1769-1782
    • Choi, S.C.1    Hobolth, A.2    Robinson, D.M.3    Kishino, H.4    Thorne, J.L.5
  • 8
    • 57149120304 scopus 로고    scopus 로고
    • Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of dna or protein sequences
    • Choi SC, Redelings BD, Thorne JL. (2008). Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of dna or protein sequences. Philos Trans R Soc Lond B Biol Sci 363: 3931-3939.
    • (2008) Philos Trans R Soc Lond B Biol Sci , vol.363 , pp. 3931-3939
    • Choi, S.C.1    Redelings, B.D.2    Thorne, J.L.3
  • 9
    • 67349264075 scopus 로고    scopus 로고
    • Estimates of natural selection due to protein tertiary structure inform the ancestry of biallelic loci
    • Choi SC, Stone EA, Kishino H, Thorne JL. (2009). Estimates of natural selection due to protein tertiary structure inform the ancestry of biallelic loci. Gene 441:45-52.
    • (2009) Gene , vol.441 , pp. 45-52
    • Choi, S.C.1    Stone, E.A.2    Kishino, H.3    Thorne, J.L.4
  • 10
    • 0036263105 scopus 로고    scopus 로고
    • Population, evolutionary and genomic consequences of interference selection
    • Comeron JM, Kreitman M. (2002). Population, evolutionary and genomic consequences of interference selection. Genetics 161: 389-410.
    • (2002) Genetics , vol.161 , pp. 389-410
    • Comeron, J.M.1    Kreitman, M.2
  • 11
    • 37349011445 scopus 로고    scopus 로고
    • The hillrobertson effect: evolutionary consequences of weak selection and linkage in finite populations
    • Comeron JM, Williford A, Kliman RM. (2008). The hillrobertson effect: evolutionary consequences of weak selection and linkage in finite populations. Heredity 100: 19-31.
    • (2008) Heredity , vol.100 , pp. 19-31
    • Comeron, J.M.1    Williford, A.2    Kliman, R.M.3
  • 12
    • 34447546660 scopus 로고    scopus 로고
    • The distribution of fitness effects of new mutations
    • Eyre-Walker A, Keightley PD. (2007). The distribution of fitness effects of new mutations. Nat Rev Genet 8:610-618.
    • (2007) Nat Rev Genet , vol.8 , pp. 610-618
    • Eyre-Walker, A.1    Keightley, P.D.2
  • 13
    • 0035998637 scopus 로고    scopus 로고
    • The common ancestor at a non-neutral locus
    • Fearnhead P. (2002). The common ancestor at a non-neutral locus. J Appl Probab 39: 38-54.
    • (2002) J Appl Probab , vol.39 , pp. 38-54
    • Fearnhead, P.1
  • 14
    • 0016110957 scopus 로고
    • The evolutionary advantage of recombination
    • Felsenstein J. (1974). The evolutionary advantage of recombination. Genetics 78: 737-756.
    • (1974) Genetics , vol.78 , pp. 737-756
    • Felsenstein, J.1
  • 15
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: a maximum likelihood approach
    • Felsenstein J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368-376.
    • (1981) J Mol Evol , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 16
    • 57349140938 scopus 로고    scopus 로고
    • Inferring the history of speciation in house mice from autosomal, x-linked, y-linked and mitochondrial genes
    • Geraldes A, Basset P, Gibson B, Smith KL, Harr B, Yu HT et al. (2008). Inferring the history of speciation in house mice from autosomal, x-linked, y-linked and mitochondrial genes. Mol Ecol 17: 5349-5363.
    • (2008) Mol Ecol , vol.17 , pp. 5349-5363
    • Geraldes, A.1    Basset, P.2    Gibson, B.3    Smith, K.L.4    Harr, B.5    Yu, H.T.6
  • 17
    • 0028168856 scopus 로고
    • A codon-based model of nucleotide substitution for proteincoding DNA sequences
    • Goldman N, Yang Z. (1994). A codon-based model of nucleotide substitution for proteincoding DNA sequences. Mol Biol Evol 11: 725-736.
    • (1994) Mol Biol Evol , vol.11 , pp. 725-736
    • Goldman, N.1    Yang, Z.2
  • 19
    • 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
  • 20
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa M, Kishino H, Yano T. (1985). Dating of 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
  • 21
    • 60549111699 scopus 로고    scopus 로고
    • Bayesian inference of population size history from multiple loci
    • Heled J, Drummond AJ. (2008). Bayesian inference of population size history from multiple loci. BMC Evol Biol 8: 289.
    • (2008) BMC Evol Biol , vol.8 , pp. 289
    • Heled, J.1    Drummond, A.J.2
  • 22
    • 0013979181 scopus 로고
    • The effect of linkage on limits to artificial selection
    • Hill WG, Robertson A. (1966). The effect of linkage on limits to artificial selection. Gene Res 8: 269-294.
    • (1966) Gene Res , vol.8 , pp. 269-294
    • Hill, W.G.1    Robertson, A.2
  • 24
    • 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
  • 25
    • 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
  • 26
    • 0014421064 scopus 로고
    • Evolutionary rate at the molecular level
    • Kimura M. (1968). Evolutionary rate at the molecular level. Nature 217: 624-626.
    • (1968) Nature , vol.217 , pp. 624-626
    • Kimura, M.1
  • 27
    • 17744413756 scopus 로고
    • Model of effectively neutral mutations in which selective constraint is incorporated
    • Kimura M. (1979). Model of effectively neutral mutations in which selective constraint is incorporated. PNAS 76:3440-3444.
    • (1979) PNAS , vol.76 , pp. 3440-3444
    • Kimura, M.1
  • 29
    • 77953771357 scopus 로고    scopus 로고
    • Statistical potentials for improved structurally constrained evolutionary models
    • Kleinman CL, Rodrigue N, Lartillot N, Philippe H. (2010). Statistical potentials for improved structurally constrained evolutionary models. Mol Biol Evol 27: 1546-1560.
    • (2010) Mol Biol Evol , vol.27 , pp. 1546-1560
    • Kleinman, C.L.1    Rodrigue, N.2    Lartillot, N.3    Philippe, H.4
  • 30
    • 2442691520 scopus 로고    scopus 로고
    • A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
    • Lartillot N, Philippe H. (2004). A Bayesian mixture model 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
  • 31
    • 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
  • 32
    • 0023263979 scopus 로고
    • The molecular clock runs more slowly in man than in apes and monkeys
    • Li WH, Tanimura M. (1987). The molecular clock runs more slowly in man than in apes and monkeys. Nature 326: 93-96.
    • (1987) Nature , vol.326 , pp. 93-96
    • Li, W.H.1    Tanimura, M.2
  • 33
    • 75749103383 scopus 로고    scopus 로고
    • Rate, molecular spectrum, and consequences of human mutation
    • Lynch M. (2010). Rate, molecular spectrum, and consequences of human mutation. PNAS 107:961-968.
    • (2010) PNAS , vol.107 , pp. 961-968
    • Lynch, M.1
  • 34
    • 0034099647 scopus 로고    scopus 로고
    • The effects of hill-robertson interference between weakly selected mutations on patterns of molecular evolution and variation
    • McVean G, Charlesworth B. (2000). The effects of hill-robertson interference between weakly selected mutations on patterns of molecular evolution and variation. Genetics 155: 929-944.
    • (2000) Genetics , vol.155 , pp. 929-944
    • McVean, G.1    Charlesworth, B.2
  • 35
    • 77949423534 scopus 로고    scopus 로고
    • Compensatory evolution in mitochondrial trnas navigates valleys of low fitness
    • Meer MV, Kondrashov AS, Artzy-Randrup Y, Kondrashov FA. (2010). Compensatory evolution in mitochondrial trnas navigates valleys of low fitness. Nature 464: 279-282.
    • (2010) Nature , vol.464 , pp. 279-282
    • Meer, M.V.1    Kondrashov, A.S.2    Artzy-Randrup, Y.3    Kondrashov, F.A.4
  • 36
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
    • Muse SV, Gaut BS. (1994). A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol 11:715-724.
    • (1994) Mol Biol Evol , vol.11 , pp. 715-724
    • Muse, S.V.1    Gaut, B.S.2
  • 37
    • 0031014102 scopus 로고    scopus 로고
    • The genealogy of samples in models with selection
    • Neuhauser C, Krone SM. (1997). The genealogy of samples in models with selection. Genetics 145: 519-534.
    • (1997) Genetics , vol.145 , pp. 519-534
    • Neuhauser, C.1    Krone, S.M.2
  • 38
    • 0043122919 scopus 로고    scopus 로고
    • Sift: Predicting amino acid changes that affect protein function
    • Ng PC, Henikoff S. (2003). Sift: Predicting amino acid changes that affect protein function. Nucleic Acids Res 31: 3812-3814.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3812-3814
    • Ng, P.C.1    Henikoff, S.2
  • 39
    • 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
  • 40
    • 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
  • 42
    • 0012088802 scopus 로고
    • Population size and rate of molecular evolution
    • Ohta T. (1972). Population size and rate of molecular evolution. J Mol Evol 1:305-314.
    • (1972) J Mol Evol , vol.1 , pp. 305-314
    • Ohta, T.1
  • 43
    • 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
  • 44
    • 0028955455 scopus 로고
    • Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory
    • Ohta T. (1995). Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory. J Mol Evol 40:56-63.
    • (1995) J Mol Evol , vol.40 , pp. 56-63
    • Ohta, T.1
  • 46
    • 54149090667 scopus 로고    scopus 로고
    • Analyzing the evolution of rna secondary structures in vertebrate introns using kimura's model of compensatory fitness interactions
    • Piskol R, Stephan W. (2008). Analyzing the evolution of rna secondary structures in vertebrate introns using kimura's model of compensatory fitness interactions. Mol Biol Evol 25: 2483-2492.
    • (2008) Mol Biol Evol , vol.25 , pp. 2483-2492
    • Piskol, R.1    Stephan, W.2
  • 47
    • 34548082528 scopus 로고    scopus 로고
    • Accumulation of slightly deleterious mutations in mitochondrial protein-coding genes of large versus small mammals
    • Popadin K, Polishchuk LV, Mamirova L, Knorre D, Gunbin K. (2007). Accumulation of slightly deleterious mutations in mitochondrial protein-coding genes of large versus small mammals. PNAS 104: 13390-13395.
    • (2007) PNAS , vol.104 , pp. 13390-13395
    • Popadin, K.1    Polishchuk, L.V.2    Mamirova, L.3    Knorre, D.4    Gunbin, K.5
  • 50
    • 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
  • 51
    • 33748126145 scopus 로고    scopus 로고
    • Assessing site-interdependent phylogenetic models of sequence evolution
    • Rodrigue N, Philippe H, Lartillot N. (2006). Assessing site-interdependent phylogenetic models of sequence evolution. Mol Biol Evol 23:1762-1775.
    • (2006) Mol Biol Evol , vol.23 , pp. 1762-1775
    • Rodrigue, N.1    Philippe, H.2    Lartillot, N.3
  • 52
    • 67649329427 scopus 로고    scopus 로고
    • Computational methods for evaluating phylogenetic models of coding sequence evolution with dependence between codons
    • Rodrigue N, Kleinman CL, Philippe H, Lartillot N. (2009). Computational methods for evaluating phylogenetic models of coding sequence evolution with dependence between codons. Mol Biol Evol 26: 1663-1676.
    • (2009) Mol Biol Evol , vol.26 , pp. 1663-1676
    • Rodrigue, N.1    Kleinman, C.L.2    Philippe, H.3    Lartillot, N.4
  • 53
    • 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. PNAS 107: 4629-4634.
    • (2010) PNAS , vol.107 , pp. 4629-4634
    • Rodrigue, N.1    Philippe, H.2    Lartillot, N.3
  • 54
    • 0025219572 scopus 로고
    • Stochastic traits of molecular evolutionacceptance of point mutations in native actin genes
    • Schöniger M, Hofacker GL, Borstnik B. (1990). Stochastic traits of molecular evolutionacceptance of point mutations in native actin genes. J Theor Biol 143: 287-306.
    • (1990) J Theor Biol , vol.143 , pp. 287-306
    • Schöniger, M.1    Hofacker, G.L.2    Borstnik, B.3
  • 55
    • 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. PNAS 102:9541-9546.
    • (2005) PNAS , vol.102 , pp. 9541-9546
    • Sella, G.1    Hirsh, A.E.2
  • 56
    • 22244437614 scopus 로고    scopus 로고
    • Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity
    • Stone EA, Sidow A. (2005). Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity. Genome Res 15: 978-986.
    • (2005) Genome Res , vol.15 , pp. 978-986
    • Stone, E.A.1    Sidow, A.2
  • 58
    • 0024313579 scopus 로고
    • Statistical method for testing the neutral mutation hypothesis by dna polymorphism
    • Tajima F. (1989). Statistical method for testing the neutral mutation hypothesis by dna polymorphism. Genetics 123: 585-595.
    • (1989) Genetics , vol.123 , pp. 585-595
    • Tajima, F.1
  • 60
    • 39749161509 scopus 로고    scopus 로고
    • Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage
    • Yang Z, Nielsen R. (2008). Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol Biol Evol 25:568-579.
    • (2008) Mol Biol Evol , vol.25 , pp. 568-579
    • Yang, Z.1    Nielsen, R.2
  • 61
    • 0034097381 scopus 로고    scopus 로고
    • Codon-substitution models for heterogeneous selection pressure at amino acid sites
    • Yang Z, Nielsen R, Goldman N, Pedersen AM. (2000). Codon-substitution models for 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.