메뉴 건너뛰기




Volumn 14, Issue 3, 1997, Pages 287-298

Evolutionary distances between nucleotide sequences based on the distribution of substitution rates among sites as estimated by parsimony

Author keywords

evolutionary distances; gamma distribution; maximum parsimony; molecular phylogeny; rate of molecular evolution; ribosomal RNA

Indexed keywords

NUCLEOTIDE; PROTEIN; RIBOSOME RNA;

EID: 0031046929     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a025764     Document Type: Article
Times cited : (36)

References (46)
  • 2
    • 0029981542 scopus 로고    scopus 로고
    • Database on the structure of large ribosomal subunit RNA
    • DE RIJK, P., Y. VAN DE PEER, and R. DE WACHTER. 1996. Database on the structure of large ribosomal subunit RNA. Nucleic Acids Res. 24:92-97.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 92-97
    • De Rijk, P.1    Van De Peer, Y.2    De Wachter, R.3
  • 3
    • 0004128472 scopus 로고
    • Cambridge University Press
    • EDWARDS, A. W. F. 1972. Likelihood. Cambridge University Press.
    • (1972) Likelihood
    • Edwards, A.W.F.1
  • 6
    • 84959747425 scopus 로고
    • Toward defining the course of evolution: Minimum change for a specific tree topology
    • FITCH, W. M. 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20:406-416.
    • (1971) Syst. Zool. , vol.20 , pp. 406-416
    • Fitch, W.M.1
  • 7
    • 0345405835 scopus 로고
    • An estimation of the number of invariable sites is necessary for the accurate estimation of the number of nucleotide substitutions since a common ancestor
    • H. GERSHOWITZ, ed. A. R. Liss, New York
    • _. 1986. An estimation of the number of invariable sites is necessary for the accurate estimation of the number of nucleotide substitutions since a common ancestor. Pp. 149-159 in H. GERSHOWITZ, ed. Evolutionary perpectives and the new genetics. A. R. Liss, New York.
    • (1986) Evolutionary Perpectives and the New Genetics , pp. 149-159
  • 8
    • 0021003230 scopus 로고
    • Estimates of DNA and protein sequence divergence: An examination of some assumptions
    • GOLDING, G. B. 1983. Estimates of DNA and protein sequence divergence: an examination of some assumptions. Mol. Biol. Evol. 1:125-142.
    • (1983) Mol. Biol. Evol. , vol.1 , pp. 125-142
    • Golding, G.B.1
  • 9
    • 0029068893 scopus 로고
    • Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites
    • GU, X., Y.-X. FU, and W.-H. LI. 1995. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol. Biol. Evol. 12:546-557.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 546-557
    • Gu, X.1    Fu, Y.-X.2    Li, W.-H.3
  • 10
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • HASEGAWA, M., H. KISHINO, and T. YANO. 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
  • 11
    • 0021017159 scopus 로고
    • The spatial distribution of fixed mutations within genes coding for proteins
    • HOLMQUIST, R., M. GOODMAN, T. CONROY, and J. CZELUSNIAK. 1983. The spatial distribution of fixed mutations within genes coding for proteins. J. Mol. Evol. 19:437-448.
    • (1983) J. Mol. Evol. , vol.19 , pp. 437-448
    • Holmquist, R.1    Goodman, M.2    Conroy, T.3    Czelusniak, J.4
  • 12
    • 0025061094 scopus 로고
    • Limitations of the evolutionary parsimony method of phylogenetic analysis
    • JIN, L., and M. NEI. 1990. Limitations of the evolutionary parsimony method of phylogenetic analysis. Mol. Biol. Evol. 7:82-102.
    • (1990) Mol. Biol. Evol. , vol.7 , pp. 82-102
    • Jin, L.1    Nei, M.2
  • 14
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • H. N. MUNRO, ed. Academic Press, New York
    • JUKES, T. H., and C. R. CANTOR. 1969. Evolution of protein molecules. Pp. 21-132 in H. N. MUNRO, ed. Mammalian protein metabolism. Academic Press, New York.
    • (1969) Mammalian Protein Metabolism , pp. 21-132
    • Jukes, T.H.1    Cantor, C.R.2
  • 15
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • KIMURA, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
    • (1980) J. Mol. Evol. , vol.16 , pp. 111-120
    • Kimura, M.1
  • 17
    • 0022507362 scopus 로고
    • Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
    • NEI, M., and T. GOJOBORI. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.
    • (1986) Mol. Biol. Evol. , vol.3 , pp. 418-426
    • Nei, M.1    Gojobori, T.2
  • 18
    • 0023498406 scopus 로고
    • Earliest phylogenetic branchings: Comparing rRNA-based evolutionary trees inferred with various techniques
    • OLSEN, G. J. 1987. Earliest phylogenetic branchings: comparing rRNA-based evolutionary trees inferred with various techniques. Cold Spring Harb. Symp. Quant. Biol. 52:825-837.
    • (1987) Cold Spring Harb. Symp. Quant. Biol. , vol.52 , pp. 825-837
    • Olsen, G.J.1
  • 19
    • 0027505613 scopus 로고
    • Ribosomal RNA: A key to phylogeny
    • OLSEN, G. J., and C. R. WOESE. 1993. Ribosomal RNA: a key to phylogeny. FASEB J. 7:113-123.
    • (1993) FASEB J. , vol.7 , pp. 113-123
    • Olsen, G.J.1    Woese, C.R.2
  • 20
    • 0028338820 scopus 로고
    • Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites
    • OTA, T., and M. NEI. 1994. Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites. J. Mol. Evol. 38:642-643.
    • (1994) J. Mol. Evol. , vol.38 , pp. 642-643
    • Ota, T.1    Nei, M.2
  • 21
    • 0024359678 scopus 로고
    • Rates of molecular evolution and the fraction of nucleotide positions free to vary
    • PALUMBI, S. R. 1989. Rates of molecular evolution and the fraction of nucleotide positions free to vary. J. Mol. Evol 29:180-187.
    • (1989) J. Mol. Evol , vol.29 , pp. 180-187
    • Palumbi, S.R.1
  • 23
    • 0026808975 scopus 로고
    • Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA
    • REEVES, J. H. 1992. Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA. J. Mol. Evol. 35:17-31.
    • (1992) J. Mol. Evol. , vol.35 , pp. 17-31
    • Reeves, J.H.1
  • 24
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • ROBINSON, D. F., and L. R. FOULDS. 1981. Comparison of phylogenetic trees. Math. Biosci. 53:131-147.
    • (1981) Math. Biosci. , vol.53 , pp. 131-147
    • Robinson, D.F.1    Foulds, L.R.2
  • 25
    • 0028230202 scopus 로고
    • Unbiased estimates of the number of nucleotide substitutions when substitution rate varies among different sites
    • RZHETSKY, A., and M. NEI. 1994. Unbiased estimates of the number of nucleotide substitutions when substitution rate varies among different sites. J. Mol. Evol. 38:295-299.
    • (1994) J. Mol. Evol. , vol.38 , pp. 295-299
    • Rzhetsky, A.1    Nei, M.2
  • 26
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • SAITOU, N., and M. NEI. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 27
    • 0024661142 scopus 로고
    • Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated
    • SHOEMAKER, J. S., and W. M. FITCH. 1989. Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated. Mol. Biol. Evol. 6:270-289.
    • (1989) Mol. Biol. Evol. , vol.6 , pp. 270-289
    • Shoemaker, J.S.1    Fitch, W.M.2
  • 28
    • 0024114801 scopus 로고
    • A note on the neighbor-joining algorithm of Saitou and Nei
    • STUDIER, J. A., and K. J. KEPPLER. 1988. A note on the neighbor-joining algorithm of Saitou and Nei. Mol. Biol. Evol. 5:729-731.
    • (1988) Mol. Biol. Evol. , vol.5 , pp. 729-731
    • Studier, J.A.1    Keppler, K.J.2
  • 29
    • 0028807391 scopus 로고
    • Among-site rate variation and phylogenetic analysis of 12S rRNA in Sigmodontine rodents
    • SULLIVAN, J., K. E. HOLSINGER, and C. SIMON. 1995. Among-site rate variation and phylogenetic analysis of 12S rRNA in Sigmodontine rodents. Mol. Biol. Evol. 12:988-1001.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 988-1001
    • Sullivan, J.1    Holsinger, K.E.2    Simon, C.3
  • 30
    • 0027157960 scopus 로고
    • Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
    • TAMURA, K., and M. NEI. 1993. 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) Mol. Biol. Evol. , vol.10 , pp. 512-526
    • Tamura, K.1    Nei, M.2
  • 31
    • 0028205953 scopus 로고
    • Relative efficiencies of the maximum-likelihood, neighbor-joining and maximum-parsimony methods when substitution rate varies with site
    • TATENO, Y., N. TAKEZAKI, and M. NEI. 1994. Relative efficiencies of the maximum-likelihood, neighbor-joining and maximum-parsimony methods when substitution rate varies with site. Mol. Biol. Evol. 11:261-277.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 261-277
    • Tateno, Y.1    Takezaki, N.2    Nei, M.3
  • 32
    • 0015219691 scopus 로고
    • Fitting discrete probability distributions to evolutionary events
    • UZZELL, T., and K. W. CORBIN. 1971. Fitting discrete probability distributions to evolutionary events. Science 172: 1089-1096.
    • (1971) Science , vol.172 , pp. 1089-1096
    • Uzzell, T.1    Corbin, K.W.2
  • 33
    • 0027313056 scopus 로고
    • Reconstructing evolution from eukaryotic small-ribosomal-subunit RNA sequences: Calibration of the molecular clock
    • VAN DE PEER, Y., J.-M. NEEFS, P. DE RIJK, and R. DE WACHTER. 1993. Reconstructing evolution from eukaryotic small-ribosomal-subunit RNA sequences: calibration of the molecular clock. J. Mol. Evol. 37:221-232.
    • (1993) J. Mol. Evol. , vol.37 , pp. 221-232
    • Van De Peer, Y.1    Neefs, J.-M.2    De Rijk, P.3    De Wachter, R.4
  • 35
    • 0029989451 scopus 로고    scopus 로고
    • The evolution of Stramenopiles and Alveolates as derived by "substitution rate calibration" of small ribosomal subunit RNA
    • VAN DE PEER, Y., G. VAN DER AUWERA, and R. DE WACHTER. 1996. The evolution of Stramenopiles and Alveolates as derived by "substitution rate calibration" of small ribosomal subunit RNA. J. Mol. Evol. 42:201-210.
    • (1996) J. Mol. Evol. , vol.42 , pp. 201-210
    • Van De Peer, Y.1    Van Der Auwera, G.2    De Wachter, R.3
  • 36
    • 0027496790 scopus 로고
    • Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA
    • WAKELEY, J. 1993. Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA. J. Mol. Evol. 37:613-623.
    • (1993) J. Mol. Evol. , vol.37 , pp. 613-623
    • Wakeley, J.1
  • 37
    • 0028297534 scopus 로고
    • Substitution-rate variation among sites and the estimation of transition bias
    • _. 1994. Substitution-rate variation among sites and the estimation of transition bias. Mol. Biol. Evol. 11:436-442.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 436-442
  • 38
    • 0023184331 scopus 로고
    • Bacterial evolution
    • WOESE, C. R. 1987. Bacterial evolution. Microbiol. Rev 51: 221-271.
    • (1987) Microbiol. Rev , vol.51 , pp. 221-271
    • Woese, C.R.1
  • 39
    • 0025300402 scopus 로고
    • Towards defining a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya
    • WOESE, C. R., O. KANDLER, and M. L. WHEELIS. 1990. Towards defining a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA 87:4576-4579.
    • (1990) Proc. Natl. Acad. Sci. USA , vol.87 , pp. 4576-4579
    • Woese, C.R.1    Kandler, O.2    Wheelis, M.L.3
  • 40
    • 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. 6:1396-1401.
    • (1993) Mol. Biol. Evol. , vol.6 , pp. 1396-1401
    • Yang, Z.1
  • 41
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • _. 1994. 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
  • 42
    • 0029067458 scopus 로고
    • Evaluation of several methods for estimating phylogenetic trees when substitution rates differ over nucleotide sites
    • _. 1995. Evaluation of several methods for estimating phylogenetic trees when substitution rates differ over nucleotide sites. J. Mol. Evol. 40:689-697.
    • (1995) J. Mol. Evol. , vol.40 , pp. 689-697
  • 43
    • 0028267146 scopus 로고
    • Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation
    • YANG, Z., N. GOLDMAN, and A. FRIDAY. 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
  • 44
    • 0029892459 scopus 로고    scopus 로고
    • Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites
    • YANG, Z., and S. KUMAR. 1996. Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites. Mol. Biol. Evol. 13: 650-659.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 650-659
    • Yang, Z.1    Kumar, S.2
  • 45
    • 0028961933 scopus 로고
    • On the use of nucleic acid sequences to infer early branchings in the tree of life
    • YANG, Z., and D. ROBERTS. 1995. On the use of nucleic acid sequences to infer early branchings 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
  • 46
    • 0029120814 scopus 로고
    • Mixed model analysis of DNA sequence evolution
    • YANG, Z., and T. WANG. 1995. Mixed model analysis of DNA sequence evolution. Biometrics 51:552-561.
    • (1995) Biometrics , vol.51 , pp. 552-561
    • Yang, Z.1    Wang, T.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.