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Volumn 42, Issue 1, 2000, Pages 25-43

Examining rates and patterns of nucleotide substitution in plants

Author keywords

Chloroplast genes; Maximum likelihood; Molecular clocks; Nucleotide substitution models; Rates of molecular evolution

Indexed keywords

CHLOROPLAST GENETICS; MITOCHONDRIAL GENETICS; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PLANT GENOME; STATISTICAL ANALYSIS;

EID: 0033955649     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1006319803002     Document Type: Article
Times cited : (132)

References (52)
  • 1
    • 0030053964 scopus 로고    scopus 로고
    • Tempo and mode of synonymous substitutions in mitochondrial DNA of primates
    • Adachi J, Hasegawa M: Tempo and mode of synonymous substitutions in mitochondrial DNA of primates. Mol Biol Evol 13: 200-208 (1996).
    • (1996) Mol Biol Evol , vol.13 , pp. 200-208
    • Adachi, J.1    Hasegawa, M.2
  • 2
    • 0027399718 scopus 로고
    • Tempo and mode of mitochondrial DNA evolution in vertebrates at the amino acid sequence level: Rapid evolution in warm-blooded vertebrates
    • Adachi J, Cao Y, Hasegawa M: Tempo and mode of mitochondrial DNA evolution in vertebrates at the amino acid sequence level: rapid evolution in warm-blooded vertebrates. J Mol Evol 36: 270-281 (1993).
    • (1993) J Mol Evol , vol.36 , pp. 270-281
    • Adachi, J.1    Cao, Y.2    Hasegawa, M.3
  • 3
    • 0029895752 scopus 로고    scopus 로고
    • Rate of rbcL gene sequence evolution and species diversification in flowering plants
    • Barraclough TG, Harvey PH, Nee S: Rate of rbcL gene sequence evolution and species diversification in flowering plants. Proc R Soc Lond B 263: 589-591 (1996).
    • (1996) Proc R Soc Lond B , vol.263 , pp. 589-591
    • Barraclough, T.G.1    Harvey, P.H.2    Nee, S.3
  • 4
    • 0026778673 scopus 로고
    • Extensive variation in evolutionary rate of rbcL gene sequences among seed plants
    • Bousquet J, Strauss SH, Doerksen AH, Price RA: Extensive variation in evolutionary rate of rbcL gene sequences among seed plants. Proc Natl Acad Sci USA 89: 7844-7848 (1992).
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 7844-7848
    • Bousquet, J.1    Strauss, S.H.2    Doerksen, A.H.3    Price, R.A.4
  • 5
    • 0028042495 scopus 로고
    • Phylogenetic relationships among the genera Taxoidiacea and Cupressaceae: Evidence from rbcL sequences
    • Brunsfeld SJ, Soltis PS, Soltis DE, Gadek PA, Quinn CJ et al.: Phylogenetic relationships among the genera Taxoidiacea and Cupressaceae: evidence from rbcL sequences. Syst Bot 19: 253-262 (1994).
    • (1994) Syst Bot , vol.19 , pp. 253-262
    • Brunsfeld, S.J.1    Soltis, P.S.2    Soltis, D.E.3    Gadek, P.A.4    Quinn, C.J.5
  • 6
    • 0003377582 scopus 로고
    • Tribal relationships in Onagraceae: Implication from rbcL sequence data
    • Conti E, Fishbach, A, Sytsma KJ: Tribal relationships in Onagraceae: implication from rbcL sequence data. Ann Miss Bot Gard 80: 672-685 (1993).
    • (1993) Ann Miss Bot Gard , vol.80 , pp. 672-685
    • Conti, E.1    Fishbach, A.2    Sytsma, K.J.3
  • 7
    • 0000347869 scopus 로고
    • Tests of separate families of hypotheses
    • Cox DR: Tests of separate families of hypotheses. Proc 4th Berkeley Symp. 1: 105-123 (1961).
    • (1961) Proc 4th Berkeley Symp. , vol.1 , pp. 105-123
    • Cox, D.R.1
  • 9
    • 0030888864 scopus 로고    scopus 로고
    • Correlated rates of synonymous site evolution among plant genomes
    • Eyre-Walker A, Gaut BS: Correlated rates of synonymous site evolution among plant genomes. Mol Biol Evol 14: 455-460 (1997).
    • (1997) Mol Biol Evol , vol.14 , pp. 455-460
    • Eyre-Walker, A.1    Gaut, B.S.2
  • 10
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein J: Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368-376 (1981).
    • (1981) J Mol Evol , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 11
    • 0030034795 scopus 로고    scopus 로고
    • A hidden Markov Model approach to variation among sites in rate of evolution
    • Felsenstein J, Churchill GA: A hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol 13: 93-104 (1996).
    • (1996) Mol Biol Evol , vol.13 , pp. 93-104
    • Felsenstein, J.1    Churchill, G.A.2
  • 12
    • 0002557518 scopus 로고    scopus 로고
    • Molecular clocks and nucleotide substitution rates in higher plants
    • Gaut BS: Molecular clocks and nucleotide substitution rates in higher plants. Evol Biol 30: 93-120 (1998).
    • (1998) Evol Biol , vol.30 , pp. 93-120
    • Gaut, B.S.1
  • 13
    • 0028244278 scopus 로고
    • Detecting substitution-rate heterogeneity among regions of a nucleotide sequence
    • Gaut BS, Weir BS: Detecting substitution-rate heterogeneity among regions of a nucleotide sequence. Mol Biol Evol 11: 620-629 (1994).
    • (1994) Mol Biol Evol , vol.11 , pp. 620-629
    • Gaut, B.S.1    Weir, B.S.2
  • 14
    • 0026469557 scopus 로고
    • Relative rates of nucleotide substitution at the rbcL locus of monocotyledonous plants
    • Gaut BS, Muse SV, Clark WD, Clegg MT: Relative rates of nucleotide substitution at the rbcL locus of monocotyledonous plants. J Mol Evol 35: 292-303 (1992).
    • (1992) J Mol Evol , vol.35 , pp. 292-303
    • Gaut, B.S.1    Muse, S.V.2    Clark, W.D.3    Clegg, M.T.4
  • 15
    • 0027611630 scopus 로고
    • Relative rates of nucleotide substitution in the chloroplast genome
    • Gaut BS, Muse SV, Clegg MT: Relative rates of nucleotide substitution in the chloroplast genome. Mol Phyl Evol 2: 89-96 (1993).
    • (1993) Mol Phyl Evol , vol.2 , pp. 89-96
    • Gaut, B.S.1    Muse, S.V.2    Clegg, M.T.3
  • 16
    • 0030816744 scopus 로고    scopus 로고
    • Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae)
    • Gaut BS, Clark LG, Wendel JF, Muse SV: Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae). Mol Biol Evol 14: 769-777 (1997).
    • (1997) Mol Biol Evol , vol.14 , pp. 769-777
    • Gaut, B.S.1    Clark, L.G.2    Wendel, J.F.3    Muse, S.V.4
  • 17
    • 0027526039 scopus 로고
    • Statistical tests of models of DNA substitution
    • Goldman N: Statistical tests of models of DNA substitution. J Mol Evol 36: 182-198 (1993).
    • (1993) J Mol Evol , vol.36 , pp. 182-198
    • Goldman, N.1
  • 18
    • 0028168856 scopus 로고
    • Codon-based model of nucleotide substitution for protein coding DNA sequences
    • Goldman N, Yang ZH: Codon-based model of nucleotide substitution for protein coding DNA sequences. Mol Biol Evol 11: 725-736 (1994).
    • (1994) Mol Biol Evol , vol.11 , pp. 725-736
    • Goldman, N.1    Yang, Z.H.2
  • 19
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa M, Kishino H, Yano T: Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22: 160-174 (1985).
    • (1985) J Mol Evol , vol.22 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 20
    • 0031436890 scopus 로고    scopus 로고
    • Phylogeny estimation and hypothesis testing using maximum likelihood
    • Huelsenbeck JP, Crandall KA: Phylogeny estimation and hypothesis testing using maximum likelihood. Annu Rev Ecol Syst 28: 437-466 (1997).
    • (1997) Annu Rev Ecol Syst , vol.28 , pp. 437-466
    • Huelsenbeck, J.P.1    Crandall, K.A.2
  • 21
    • 0030902563 scopus 로고    scopus 로고
    • Phylogenetic methods come of age: Testing hypotheses in an evolutionary context
    • Huelsenbeck JP, Rannala B: Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 276: 227-232 (1997).
    • (1997) Science , vol.276 , pp. 227-232
    • Huelsenbeck, J.P.1    Rannala, B.2
  • 22
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • Munro HN (ed), Academic Press, New York
    • Jukes TH, Cantor CR: Evolution of protein molecules. In: Munro HN (ed), Mammalian Protein Metabolism, pp. 21-32. Academic Press, New York (1969).
    • (1969) Mammalian Protein Metabolism , pp. 21-32
    • Jukes, T.H.1    Cantor, C.R.2
  • 23
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • Kimura M: A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111-120 (1980).
    • (1980) J Mol Evol , vol.16 , pp. 111-120
    • Kimura, M.1
  • 24
    • 0030914649 scopus 로고    scopus 로고
    • Molecular evolution of angiosperm mitochondrial introns and exons
    • Laroche J, Li P, Maggia L, Bousquet J: Molecular evolution of angiosperm mitochondrial introns and exons. Proc Natl Acad Sci USA 94: 5722-5727 (1997).
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 5722-5727
    • Laroche, J.1    Li, P.2    Maggia, L.3    Bousquet, J.4
  • 25
    • 0026486403 scopus 로고
    • Relative-rate test for nucleotide substitutions between two lineages
    • Li P, Bousquet J: Relative-rate test for nucleotide substitutions between two lineages. Mol Biol Evol 9: 1185-1189 (1992).
    • (1992) Mol Biol Evol , vol.9 , pp. 1185-1189
    • Li, P.1    Bousquet, J.2
  • 26
    • 0029784030 scopus 로고    scopus 로고
    • Prolonged final extension time increases cloning efficiency of PCR products
    • Li Q, Guy C: Prolonged final extension time increases cloning efficiency of PCR products. Biotechniques 21: 192-196 (1996).
    • (1996) Biotechniques , vol.21 , pp. 192-196
    • Li, Q.1    Guy, C.2
  • 27
    • 0022005270 scopus 로고
    • A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes
    • Li W-H, Wu C-I, Luo C-C: A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol 2: 150-174 (1985).
    • (1985) Mol Biol Evol , vol.2 , pp. 150-174
    • Li, W.-H.1    Wu, C.-I.2    Luo, C.-C.3
  • 28
    • 0023074036 scopus 로고
    • An evaluation of the molecular clock hypothesis using mammalian DNA sequences
    • Li W-H, Tanimura M, Sharp P: An evaluation of the molecular clock hypothesis using mammalian DNA sequences. J Mol Evol 25: 330-342 (1987).
    • (1987) J Mol Evol , vol.25 , pp. 330-342
    • Li, W.-H.1    Tanimura, M.2    Sharp, P.3
  • 29
    • 0028900996 scopus 로고
    • Evolutionary analyses of DNA sequences subject to constraints on secondary structure
    • Muse SV: Evolutionary analyses of DNA sequences subject to constraints on secondary structure. Genetics 139: 1429-1439 (1995).
    • (1995) Genetics , vol.139 , pp. 1429-1439
    • Muse, S.V.1
  • 30
    • 0030054305 scopus 로고    scopus 로고
    • Estimating synonymous and nonsynonymous substitution rates
    • Muse SV: Estimating synonymous and nonsynonymous substitution rates. Mol Biol Evol 13: 105-114 (1996).
    • (1996) Mol Biol Evol , vol.13 , pp. 105-114
    • Muse, S.V.1
  • 31
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
    • Muse SV, Gaut BS: A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol 11: 715-724 (1994).
    • (1994) Mol Biol Evol , vol.11 , pp. 715-724
    • Muse, S.V.1    Gaut, B.S.2
  • 32
    • 0030984551 scopus 로고    scopus 로고
    • Comparing patterns of nucleotide patterns among chloroplast loci using the relative ratio test
    • Muse SV, Gaut BS: Comparing patterns of nucleotide patterns among chloroplast loci using the relative ratio test. Genetics 146: 393-399 (1997).
    • (1997) Genetics , vol.146 , pp. 393-399
    • Muse, S.V.1    Gaut, B.S.2
  • 33
    • 0026670564 scopus 로고
    • Testing for equality of evolutionary rates
    • Muse SV, Weir BS: Testing for equality of evolutionary rates. Genetics 132: 269-276 (1992).
    • (1992) Genetics , vol.132 , pp. 269-276
    • Muse, S.V.1    Weir, B.S.2
  • 34
    • 0028275088 scopus 로고
    • High rates of nucleotide substitution rate in nuclear small-subunit (18S) rDNA from holoparasitic flowering plants
    • Nickrent DL, Starr EM: High rates of nucleotide substitution rate in nuclear small-subunit (18S) rDNA from holoparasitic flowering plants. J Mol Evol 39: 62-70 (1994).
    • (1994) J Mol Evol , vol.39 , pp. 62-70
    • Nickrent, D.L.1    Starr, E.M.2
  • 35
    • 0002880305 scopus 로고    scopus 로고
    • Molecular phylogenetic and evolutionary studies of parasitic plants
    • Soltis PS, Doyle JJ, Soltis DE (eds), Kluwer Academic Publishers, Boston
    • Nickrent DL, dePamphilis CW, Wolfe AD, Colwell AE, Young ND et al.: Molecular phylogenetic and evolutionary studies of parasitic plants. In: Soltis PS, Doyle JJ, Soltis DE (eds), Molecular Systematics of Plants 2: DNA sequencing, pp. 211-241. Kluwer Academic Publishers, Boston (1998).
    • (1998) Molecular Systematics of Plants 2: DNA Sequencing , pp. 211-241
    • Nickrent, D.L.1    DePamphilis, C.W.2    Wolfe, A.D.3    Colwell, A.E.4    Young, N.D.5
  • 36
    • 0031880125 scopus 로고    scopus 로고
    • A codon-based model designed to describe lentiviral evolution
    • Pederson A-M: A codon-based model designed to describe lentiviral evolution. Mol Biol Evol 15: 1069-1081 (1998).
    • (1998) Mol Biol Evol , vol.15 , pp. 1069-1081
    • Pederson, A.-M.1
  • 37
    • 0025267792 scopus 로고
    • The general stochastic model of nucleotide substitution
    • Rodriguez F, Oliver JF, Marin A, Medina JR: The general stochastic model of nucleotide substitution. J Theor Biol 142: 485-501 (1990).
    • (1990) J Theor Biol , vol.142 , pp. 485-501
    • Rodriguez, F.1    Oliver, J.F.2    Marin, A.3    Medina, J.R.4
  • 38
    • 0014186296 scopus 로고
    • Immunological time scale for hominid evolution
    • Sarich VM, Wilson AC: Immunological time scale for hominid evolution. Science 158: 1200-1203 (1967).
    • (1967) Science , vol.158 , pp. 1200-1203
    • Sarich, V.M.1    Wilson, A.C.2
  • 39
    • 0039863095 scopus 로고
    • Chloroplast DNA variation and evolution in the Juglandaceae
    • Smith JF, Doyle JJ: Chloroplast DNA variation and evolution in the Juglandaceae. Am J Bot 78: 730 (1986).
    • (1986) Am J Bot , vol.78 , pp. 730
    • Smith, J.F.1    Doyle, J.J.2
  • 40
    • 0002408597 scopus 로고
    • Coevolution of grasses and herbivores
    • Stebbins GL: Coevolution of grasses and herbivores. Ann Miss Bot Gard 68: 75-86 (1981).
    • (1981) Ann Miss Bot Gard , vol.68 , pp. 75-86
    • Stebbins, G.L.1
  • 41
    • 0001336205 scopus 로고    scopus 로고
    • Phylogenetic inference
    • Hillis DM, Mortiz C, Mable BK (eds), Sinauer Associates, Inc., Sunderland, MA
    • Swofford DL, Olsen GJ, Waddell PJ, Hillis DM: Phylogenetic inference. In: Hillis DM, Mortiz C, Mable BK (eds), Molecular Systematics, pp. 407-514. Sinauer Associates, Inc., Sunderland, MA (1996).
    • (1996) Molecular Systematics , pp. 407-514
    • Swofford, D.L.1    Olsen, G.J.2    Waddell, P.J.3    Hillis, D.M.4
  • 42
    • 0027157960 scopus 로고
    • Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
    • 41a. Tamura K, Nei M: Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10: 512-526 (1993).
    • (1993) Mol Biol Evol , vol.10 , pp. 512-526
    • Tamura, K.1    Nei, M.2
  • 43
    • 0002671410 scopus 로고
    • Some probabilistic and statistical problems in the analysis of DNA sequences
    • Miura RM (ed.), American Mathematic Society, Providence, RI
    • Tavare S: Some probabilistic and statistical problems in the analysis of DNA sequences. In: Miura RM (ed.), Lecture on Mathematics in the Life Sciences, pp. 57-86. American Mathematic Society, Providence, RI (1986).
    • (1986) Lecture on Mathematics in the Life Sciences , pp. 57-86
    • Tavare, S.1
  • 44
    • 0029985399 scopus 로고    scopus 로고
    • Combining protein evolution and secondary structure
    • Thorne JL, Goldman N, Jones DT: Combining protein evolution and secondary structure. Mol Biol Evol 13: 666-673 (1996).
    • (1996) Mol Biol Evol , vol.13 , pp. 666-673
    • Thorne, J.L.1    Goldman, N.2    Jones, D.T.3
  • 45
    • 0028874337 scopus 로고
    • Neighbor joining and maximum likelihood with RNA sequences: Addressing the interdependence of sites
    • Tillier ERM, Collins RA: Neighbor joining and maximum likelihood with RNA sequences: addressing the interdependence of sites. Mol Biol Evol 12: 7-15 (1995).
    • (1995) Mol Biol Evol , vol.12 , pp. 7-15
    • Tillier, E.R.M.1    Collins, R.A.2
  • 46
    • 0023462635 scopus 로고
    • Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast and nuclear DNAs
    • Wolfe KH, Li W-H, Sharp PM: Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast and nuclear DNAs. Proc Natl Acad Sci USA 84: 9054-9058 (1987).
    • (1987) Proc Natl Acad Sci USA , vol.84 , pp. 9054-9058
    • Wolfe, K.H.1    Li, W.-H.2    Sharp, P.M.3
  • 47
    • 0024712231 scopus 로고
    • Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data
    • Wolfe KH, Gouy M, Yang Y-W, Sharp PM, Li W-H: Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc Natl Acad Sci USA 86: 6201-6205 (1989).
    • (1989) Proc Natl Acad Sci USA , vol.86 , pp. 6201-6205
    • Wolfe, K.H.1    Gouy, M.2    Yang, Y.-W.3    Sharp, P.M.4    Li, W.-H.5
  • 48
    • 0000175619 scopus 로고
    • Rates of synonymous substitution in plant nuclear genes
    • Wolfe KH, Sharp PM, Li W-H: Rates of synonymous substitution in plant nuclear genes. J Mol Evol 29: 208-211 (1989).
    • (1989) J Mol Evol , vol.29 , pp. 208-211
    • Wolfe, K.H.1    Sharp, P.M.2    Li, W.-H.3
  • 49
    • 0000378875 scopus 로고
    • Evidence for higher rates of nucleotide substitution in rodents than in man
    • Wu C-I, Li W-H: Evidence for higher rates of nucleotide substitution in rodents than in man. Proc Natl Acad Sci USA 82: 1741-1745 (1985).
    • (1985) Proc Natl Acad Sci USA , vol.82 , pp. 1741-1745
    • Wu, C.-I.1    Li, W.-H.2
  • 50
    • 0027132974 scopus 로고
    • Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
    • Yang Z: Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol 10: 1396-1401 (1993).
    • (1993) Mol Biol Evol , vol.10 , pp. 1396-1401
    • Yang, Z.1
  • 51
    • 0028214103 scopus 로고
    • Estimating the pattern of nucleotide substitution
    • Yang Z: Estimating the pattern of nucleotide substitution. J Mol Evol 39: 105-111 (1994).
    • (1994) J Mol Evol , vol.39 , pp. 105-111
    • Yang, Z.1
  • 52
    • 0028813337 scopus 로고
    • A space-time process model for the evolution of DNA sequences
    • Yang Z: A space-time process model for the evolution of DNA sequences. Genetics 139: 993-1005 (1995).
    • (1995) Genetics , vol.139 , pp. 993-1005
    • Yang, Z.1


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