메뉴 건너뛰기




Volumn 48, Issue 2, 1999, Pages 218-235

Phylogeny of organisms investigated by the base-pair changes in the stem regions of small and large ribosomal subunit RNAs

Author keywords

Base pairs; Divergence time; Functional constraint; Molecular clock; Mutation rate; Phylogenetic tree; Ribosomal RNA

Indexed keywords

ANIMAL CELL; ARTICLE; BASE PAIRING; CALCULATION; DNA DAMAGE; EVOLUTION; GENE MUTATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHOTOSYNTHESIS; PHYLOGENY; RIBOSOME;

EID: 0032902335     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006461     Document Type: Article
Times cited : (20)

References (45)
  • 1
    • 0024474078 scopus 로고
    • A conserved 3′→5′ exonuclease active site in prokaryotic and eukaryotic DNA polymerases
    • Bernad A, Blanco L, Lazaro JM, Martin G, Salas M (1989) A conserved 3′→5′ exonuclease active site in prokaryotic and eukaryotic DNA polymerases. Cell 59:219-228
    • (1989) Cell , vol.59 , pp. 219-228
    • Bernad, A.1    Blanco, L.2    Lazaro, J.M.3    Martin, G.4    Salas, M.5
  • 2
    • 0015991182 scopus 로고
    • Evolution of ecosystems
    • Cloud PE Jr (1974) Evolution of ecosystems. Am Sci 62:54-66
    • (1974) Am Sci , vol.62 , pp. 54-66
    • Cloud P.E., Jr.1
  • 4
    • 0021707493 scopus 로고
    • Quantitation of base substitutions in eukaryotic 5S rRNA: Selection for the maintenance of RNA secondary structure
    • Curtiss WC, Vournakis JN (1984) Quantitation of base substitutions in eukaryotic 5S rRNA: Selection for the maintenance of RNA secondary structure. J Mol Evol 20:351-361
    • (1984) J Mol Evol , vol.20 , pp. 351-361
    • Curtiss, W.C.1    Vournakis, J.N.2
  • 6
    • 0030765449 scopus 로고    scopus 로고
    • Database on the structure of large ribosomal subunit RNA
    • De Rijk P, Van de Peer Y, De Wachter R (1997) Database on the structure of large ribosomal subunit RNA. Nucleic Acids Res 25:117-123
    • (1997) Nucleic Acids Res , vol.25 , pp. 117-123
    • De Rijk, P.1    Van De Peer, Y.2    De Wachter, R.3
  • 7
    • 0015162882 scopus 로고
    • The structure of cytochrome c and the rate of molecular evolution
    • Dickerson RE (1971) The structure of cytochrome c and the rate of molecular evolution. J Mol Evol 1:26-45
    • (1971) J Mol Evol , vol.1 , pp. 26-45
    • Dickerson, R.E.1
  • 8
    • 0003242435 scopus 로고
    • The jackknife, the bootstrap, and other resampling plans
    • Society for Industrial and Applied Mathematics, Philadelphia, PA
    • Efron B (1982) The jackknife, the bootstrap, and other resampling plans. CBMS-NSF Regional Conference Series in Applied Mathematics No 38. Society for Industrial and Applied Mathematics, Philadelphia, PA
    • (1982) CBMS-NSF Regional Conference Series in Applied Mathematics No 38
    • Efron, B.1
  • 9
    • 0002476512 scopus 로고
    • Structural map of 23S rRNA
    • Hill WE, Moore PB, Dahlberg A, Schlessinger D, Garrett RA, Warner JR (eds). American Society for Microbiology
    • Egebjerg J, Larsen N, Garrett RA (1989) Structural map of 23S rRNA. In: Hill WE, Moore PB, Dahlberg A, Schlessinger D, Garrett RA, Warner JR (eds) The ribosome, structure, function, and evolution. American Society for Microbiology, pp 168-179
    • (1989) The Ribosome, Structure, Function, and Evolution , pp. 168-179
    • Egebjerg, J.1    Larsen, N.2    Garrett, R.A.3
  • 10
    • 0001192522 scopus 로고
    • Distance methods and the approximation of most-parsimonious trees
    • Faith DP (1985) Distance methods and the approximation of most-parsimonious trees. Syst Zool 34:312-325
    • (1985) Syst Zool , vol.34 , pp. 312-325
    • Faith, D.P.1
  • 11
    • 0000472542 scopus 로고
    • Estimating phylogenic trees from distance matrices
    • Farris JS (1972) Estimating phylogenic trees from distance matrices. Am Nat 106:645-668
    • (1972) Am Nat , vol.106 , pp. 645-668
    • Farris, J.S.1
  • 12
    • 0030696044 scopus 로고    scopus 로고
    • Determining divergence times with a protein clock: Update and reevaluation
    • Feng D-F, Cho G, Doolittle RF (1997) Determining divergence times with a protein clock: Update and reevaluation. Proc Natl Acad Sci USA 94:13028-13033.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 13028-13033
    • Feng, D.-F.1    Cho, G.2    Doolittle, R.F.3
  • 13
    • 0014211361 scopus 로고
    • Construction of phylogenic tree
    • Fitch WM, Margoliash E (1967) Construction of phylogenic tree. Science 155:279-284
    • (1967) Science , vol.155 , pp. 279-284
    • Fitch, W.M.1    Margoliash, E.2
  • 14
    • 0019752439 scopus 로고
    • A non-sequential method for constructing trees and hierarchial classification
    • Fitch WM (1981) A non-sequential method for constructing trees and hierarchial classification. J Mol Evol 18:30-37
    • (1981) J Mol Evol , vol.18 , pp. 30-37
    • Fitch, W.M.1
  • 15
    • 0017347967 scopus 로고
    • Comparative cataloging of 16S ribosomal ribonucleic acid: Molecular approach to prokaryotic systematics
    • Fox GE, Peckman KJ, Woese CR (1977) Comparative cataloging of 16S ribosomal ribonucleic acid: Molecular approach to prokaryotic systematics. Int J Syst Bacteriol 27:44-57
    • (1977) Int J Syst Bacteriol , vol.27 , pp. 44-57
    • Fox, G.E.1    Peckman, K.J.2    Woese, C.R.3
  • 16
    • 0000964597 scopus 로고
    • Analogous microbial forms in recent subaerial habitats and in Precambrian chert: Gloeothece coerulea (Geitler) and Eosynechococcus moorei (Hofmann)
    • Golubic S, Campbell SE (1979) Analogous microbial forms in recent subaerial habitats and in Precambrian chert: Gloeothece coerulea (Geitler) and Eosynechococcus moorei (Hofmann). Precambrian Res 8:201-217
    • (1979) Precambrian Res , vol.8 , pp. 201-217
    • Golubic, S.1    Campbell, S.E.2
  • 17
    • 0016984263 scopus 로고
    • Carbon and sulfur isotope abundance in Archean iron formations and early Precambrian life
    • Goodwin AM, Monster J, Thode HG (1976) Carbon and sulfur isotope abundance in Archean iron formations and early Precambrian life. Eco Geol 71:870-891
    • (1976) Eco Geol , vol.71 , pp. 870-891
    • Goodwin, A.M.1    Monster, J.2    Thode, H.G.3
  • 18
    • 0020038147 scopus 로고
    • The phylogenic structure of the metabacteria
    • Hori H, Itoh T, Osawa S (1982) The phylogenic structure of the metabacteria. Zbl Bakt Hyg I Abt Orig C3:18-30
    • (1982) Zbl Bakt Hyg I Abt Orig , vol.C3 , pp. 18-30
    • Hori, H.1    Itoh, T.2    Osawa, S.3
  • 19
    • 0018369831 scopus 로고
    • Evolutionary change in 5S RNA secondary structure and a phylogenic tree of 54 5S RNA species
    • Hori H, Osawa S (1979) Evolutionary change in 5S RNA secondary structure and a phylogenic tree of 54 5S RNA species. Proc Natl Acad Sci USA 76:381-385
    • (1979) Proc Natl Acad Sci USA , vol.76 , pp. 381-385
    • Hori, H.1    Osawa, S.2
  • 20
    • 0024617798 scopus 로고
    • Rapid evolutionary repair of base mispairings in stem regions of eukaryotic 5S rRNA
    • Horimoto K, Otsuka J, Kunisawa T (1989) Rapid evolutionary repair of base mispairings in stem regions of eukaryotic 5S rRNA. Protein Seq Data Anal 2:93-99
    • (1989) Protein Seq Data Anal , vol.2 , pp. 93-99
    • Horimoto, K.1    Otsuka, J.2    Kunisawa, T.3
  • 21
    • 0028318869 scopus 로고
    • Amino acid sequence motifs essential to 3′→5′ exonuclease activity of Escherichia coli DNA polymerase II
    • Ishino Y, Iwasaki H, Kato I, Shinagawa H (1994) Amino acid sequence motifs essential to 3′→5′ exonuclease activity of Escherichia coli DNA polymerase II. J Biol Chem 269:14655-14660
    • (1994) J Biol Chem , vol.269 , pp. 14655-14660
    • Ishino, Y.1    Iwasaki, H.2    Kato, I.3    Shinagawa, H.4
  • 22
    • 0025766848 scopus 로고
    • Compilation and alignment of DNA polymerase sequences
    • Ito J, Braithwaite DK (1991) Compilation and alignment of DNA polymerase sequences. Nucleic Acids Res 19:4045-4057
    • (1991) Nucleic Acids Res , vol.19 , pp. 4045-4057
    • Ito, J.1    Braithwaite, D.K.2
  • 23
    • 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
  • 24
    • 0014553632 scopus 로고
    • The rate of molecular evolution considered from the standpoint of population genetics
    • Kimura M (1969) The rate of molecular evolution considered from the standpoint of population genetics. Proc Natl Acad Sci USA 63:1181-1188
    • (1969) Proc Natl Acad Sci USA , vol.63 , pp. 1181-1188
    • Kimura, M.1
  • 25
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences
    • Kimura M (1980) A simple method for estimating evolutionary rate 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
  • 26
    • 0001464973 scopus 로고
    • Estimation of evolutionary distances between homologous nucleotide sequences
    • Kimura M (1981) Estimation of evolutionary distances between homologous nucleotide sequences. Proc Natl Acad Sci USA 78:454-458
    • (1981) Proc Natl Acad Sci USA , vol.78 , pp. 454-458
    • Kimura, M.1
  • 27
    • 0021014901 scopus 로고
    • Phylogeny of Protozoa deduced from 5S rRNA sequences
    • Kumazaki T, Hori H, Osawa S (1983) Phylogeny of Protozoa deduced from 5S rRNA sequences. J Mol Evol 91:411-419
    • (1983) J Mol Evol , vol.91 , pp. 411-419
    • Kumazaki, T.1    Hori, H.2    Osawa, S.3
  • 29
    • 0001753988 scopus 로고
    • Primary structure and evolution of cytochrome c
    • Margoliash E (1963) Primary structure and evolution of cytochrome c. Proc Natl Acad Sci USA 50:672-679
    • (1963) Proc Natl Acad Sci USA , vol.50 , pp. 672-679
    • Margoliash, E.1
  • 31
    • 0031581662 scopus 로고    scopus 로고
    • A theoretical study on the nucleotide changes under a definite functional constraint of forming stable base-pairs in the stem regions of ribosomal RNAs; its application to the phylogeny of eukaryotes
    • Otsuka J, Nakano T, Terai G (1997a) A theoretical study on the nucleotide changes under a definite functional constraint of forming stable base-pairs in the stem regions of ribosomal RNAs; Its application to the phylogeny of eukaryotes. J Theor Biol 184:171-186
    • (1997) J Theor Biol , vol.184 , pp. 171-186
    • Otsuka, J.1    Nakano, T.2    Terai, G.3
  • 32
    • 0030756294 scopus 로고    scopus 로고
    • A theoretical method for evaluating the relative importance of positive selection and neutral drift from observed base changes
    • Otsuka J, Fukuchi S, Kikuchi N (1997b) A theoretical method for evaluating the relative importance of positive selection and neutral drift from observed base changes. J Mol Evol 45:178-192
    • (1997) J Mol Evol , vol.45 , pp. 178-192
    • Otsuka, J.1    Fukuchi, S.2    Kikuchi, N.3
  • 33
    • 0002574521 scopus 로고
    • rRNA: From structure to function
    • Hill WE, Moore PB, Dahlberg A, Schlessinger D, Garrett RA, Warner JR (eds). American Society for Microbiology, Washington DC
    • Raue HA, Muster W, Rutgers CA, Riet JV, Planta RJ (1989) rRNA: from structure to function. In: Hill WE, Moore PB, Dahlberg A, Schlessinger D, Garrett RA, Warner JR (eds) The ribosome, structure, function, and evolution. American Society for Microbiology, Washington DC
    • (1989) The Ribosome, Structure, Function, and Evolution
    • Raue, H.A.1    Muster, W.2    Rutgers, C.A.3    Riet, J.V.4    Planta, R.J.5
  • 34
    • 0002056065 scopus 로고
    • Primary productivity in an early Archaen microbial ecosystem
    • Reimer TO, Barghoorn ES, Margulis L (1979) Primary productivity in an early Archaen microbial ecosystem. Precambrian Res 9:93-104
    • (1979) Precambrian Res , vol.9 , pp. 93-104
    • Reimer, T.O.1    Barghoorn, E.S.2    Margulis, L.3
  • 35
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou N, Nei M (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
  • 36
    • 0027368923 scopus 로고
    • Cloning and expression of cDNA for a human enzyme that hydrolyzes 8-oxo-dGTP, a mutagenic substrate for DNA synthesis
    • Sakumi K, Furuichi M, Tsuzuki T, Kakuma T, Kawabata S-I, Maki H, Sekiguchi M (1993) Cloning and expression of cDNA for a human enzyme that hydrolyzes 8-oxo-dGTP, a mutagenic substrate for DNA synthesis. J Biol Chem 268:23524-23530
    • (1993) J Biol Chem , vol.268 , pp. 23524-23530
    • Sakumi, K.1    Furuichi, M.2    Tsuzuki, T.3    Kakuma, T.4    Kawabata, S.-I.5    Maki, H.6    Sekiguchi, M.7
  • 37
    • 0000491446 scopus 로고
    • Additive similarity trees
    • Sattath S, Tversky A (1977) Additive similarity trees. Psychometrica 42:319-345
    • (1977) Psychometrica , vol.42 , pp. 319-345
    • Sattath, S.1    Tversky, A.2
  • 38
    • 0020363837 scopus 로고
    • Accuracy of estimated phylogenetic trees from molecular data. I. Distantly related species
    • Tateno Y, Nei M, Tajima F (1982) Accuracy of estimated phylogenetic trees from molecular data. I. Distantly related species. J Mol Evol 18:387-404
    • (1982) J Mol Evol , vol.18 , pp. 387-404
    • Tateno, Y.1    Nei, M.2    Tajima, F.3
  • 39
    • 0028509254 scopus 로고
    • TREECON for Windows: A software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment
    • Van de Peer Y, De Wachter R (1994) TREECON for Windows: A software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10:569-570
    • (1994) Comput Appl Biosci , vol.10 , pp. 569-570
    • Van De Peer, Y.1    De Wachter, R.2
  • 41
    • 0023810314 scopus 로고
    • The 5S ribosomal RNA sequences of a red algal rhodoplast and a gymnosperm chloroplast: Implication for the evolution of plastids and cyanobacteria
    • Van den Eynde H, De Baere R, De Roeck E, Van de Peer Y, Vandenberghe A, Willekens P, De Wachter R (1988) The 5S ribosomal RNA sequences of a red algal rhodoplast and a gymnosperm chloroplast: Implication for the evolution of plastids and cyanobacteria. J Mol Evol 27:126-132
    • (1988) J Mol Evol , vol.27 , pp. 126-132
    • Van Den Eynde, H.1    De Baere, R.2    De Roeck, E.3    Van De Peer, Y.4    Vandenberghe, A.5    Willekens, P.6    De Wachter, R.7
  • 42
    • 0017956171 scopus 로고
    • Protist classification and the kingdoms of organisms
    • Whittaker RH, Margulis L (1978) Protist classification and the kingdoms of organisms. BioSystems 10:3-18
    • (1978) BioSystems , vol.10 , pp. 3-18
    • Whittaker, R.H.1    Margulis, L.2
  • 43
    • 0023184331 scopus 로고
    • Bacterial evolution
    • Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221-271
    • (1987) Microbiol Rev , vol.51 , pp. 221-271
    • Woese, C.R.1
  • 45
    • 0002331493 scopus 로고
    • Molecular disease, evolution and genetic heterogeneity
    • Kasha M and Pullman B (eds). Academic Press, New York
    • Zuckerkandl E, Pauling L (1962) Molecular disease, evolution and genetic heterogeneity. In: Kasha M and Pullman B (eds) Horizons in biochemistry. Academic Press, New York, pp 189-225
    • (1962) Horizons in Biochemistry , pp. 189-225
    • Zuckerkandl, E.1    Pauling, L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.