메뉴 건너뛰기




Volumn 20, Issue 2, 2003, Pages 182-189

Identifying site-specific substitution rates

Author keywords

Human mitochondrial DNA; Maximum likelihood; Sequence evolution; Site specific substitution rates; Tree reconstruction

Indexed keywords

MITOCHONDRIAL DNA;

EID: 0037329091     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msg019     Document Type: Article
Times cited : (26)

References (36)
  • 1
    • 0019423856 scopus 로고
    • Sequence and organization of the human mitochondrial genome
    • Anderson, S., A. T. Bankier, B. G. Barrell, et al. (14 co-authors). 1981. Sequence and organization of the human mitochondrial genome. Nature 290:457-465.
    • (1981) Nature , vol.290 , pp. 457-465
    • Anderson, S.1    Bankier, A.T.2    Barrell, B.G.3
  • 2
    • 0030056912 scopus 로고    scopus 로고
    • The impact of population expansion and mutation rate heterogeneity on DNA sequence polymorphism
    • Aris-Brosou, S., and L. Excoffier. 1996. The impact of population expansion and mutation rate heterogeneity on DNA sequence polymorphism. Mol. Biol. Evol. 13:494-504.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 494-504
    • Aris-Brosou, S.1    Excoffier, L.2
  • 3
    • 0033646639 scopus 로고    scopus 로고
    • Transcription and replication of mitochondrial DNA
    • Clayton, D. A. 2000. Transcription and replication of mitochondrial DNA. Hum. Reprod. 15:11-17.
    • (2000) Hum. Reprod. , vol.15 , pp. 11-17
    • Clayton, D.A.1
  • 5
    • 0032873641 scopus 로고    scopus 로고
    • Substitution rate variation among sites in mitochondrial hypervariable region i of humans and chimpanzees
    • Excoffier, L., and Z. Yang. 1999. Substitution rate variation among sites in mitochondrial hypervariable region i of humans and chimpanzees. Mol. Biol. Evol. 16:1357-1368.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1357-1368
    • Excoffier, L.1    Yang, Z.2
  • 6
    • 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
  • 7
    • 0015076741 scopus 로고
    • The nonidentity of invariable positions in the cytochomes c of different species
    • Fitch, W. M. 1971. The nonidentity of invariable positions in the cytochomes c of different species. Biochem. Genet. 5:231-241.
    • (1971) Biochem. Genet. , vol.5 , pp. 231-241
    • Fitch, W.M.1
  • 8
    • 0035029534 scopus 로고    scopus 로고
    • Maximum-likelihood phylogenetic analysis under a covarion-like model
    • Galtier, N. 2001. Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol. Biol. Evol. 18:866-873.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 866-873
    • Galtier, N.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
    • 0027428406 scopus 로고
    • Toward a more accurate time scale for the human mitochondrial DNA tree
    • Hasegawa, M., A. D. Rienzo, T. D. Kocher, and A. C. Wilson. 1993. Toward a more accurate time scale for the human mitochondrial DNA tree. J. Mol. Evol. 37:347-354.
    • (1993) J. Mol. Evol. , vol.37 , pp. 347-354
    • Hasegawa, M.1    Rienzo, A.D.2    Kocher, T.D.3    Wilson, A.C.4
  • 11
    • 0001935493 scopus 로고
    • Gene genealogies and the coalescent process
    • Hudson, R. R. 1991. Gene genealogies and the coalescent process. Oxf. Surv. Evol. Biol. 7:1-44.
    • (1991) Oxf. Surv. Evol. Biol. , vol.7 , pp. 1-44
    • Hudson, R.R.1
  • 12
    • 0036097894 scopus 로고    scopus 로고
    • Testing a covariotide model of DNA substitution
    • Huelsenbeck, J. P. 2002. Testing a covariotide model of DNA substitution. Mol. Biol. Evol. 19:698-707.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 698-707
    • Huelsenbeck, J.P.1
  • 13
    • 0034619822 scopus 로고    scopus 로고
    • Mitochondrial genome variation and the origin of modem humans
    • Ingman, M., H. Kaessmann, S. Pääbo, and U. Gyllensten. 2000. Mitochondrial genome variation and the origin of modem humans. Nature 408:708-712.
    • (2000) Nature , vol.408 , pp. 708-712
    • Ingman, M.1    Kaessmann, H.2    Pääbo, S.3    Gyllensten, U.4
  • 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
    • 0029930086 scopus 로고    scopus 로고
    • Modelling nucleotide evolution: A heterogeneous rate analysis
    • Kelly, C., and J. Rice. 1996. Modelling nucleotide evolution: a heterogeneous rate analysis. Math. Biosci. 133:85-109.
    • (1996) Math. Biosci. , vol.133 , pp. 85-109
    • Kelly, C.1    Rice, J.2
  • 18
    • 0036134757 scopus 로고    scopus 로고
    • Heterotachy, an important process of protein evolution
    • Lopez, P., D. Casane, and H. Philippe. 2002. Heterotachy, an important process of protein evolution. Mol. Biol. Evol. 19:1-7.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 1-7
    • Lopez, P.1    Casane, D.2    Philippe, H.3
  • 19
    • 0032779612 scopus 로고    scopus 로고
    • Pattern of nucleotide substitution and rate heterogeneity in the hypervariable regions I and II of human mtDNA
    • Meyer, S., G. Weiss, and A. von Haeseler. 1999. Pattern of nucleotide substitution and rate heterogeneity in the hypervariable regions I and II of human mtDNA. Genetics 152:1103-1110.
    • (1999) Genetics , vol.152 , pp. 1103-1110
    • Meyer, S.1    Weiss, G.2    Von Haeseler, A.3
  • 20
    • 0028922906 scopus 로고
    • Testing the covarion hypothesis of molecular evolution
    • Miyamoto, M. M., and W. M. Fitch. 1995. Testing the covarion hypothesis of molecular evolution. Mol. Biol. Evol. 12:503-513.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 503-513
    • Miyamoto, M.M.1    Fitch, W.M.2
  • 21
    • 0031153858 scopus 로고    scopus 로고
    • Site-by-site estimation of the rate of substitution and the correlation of rates in mitochondrial DNA
    • Nielsen, R. 1997. Site-by-site estimation of the rate of substitution and the correlation of rates in mitochondrial DNA. Syst. Biol. 46:346-353.
    • (1997) Syst. Biol. , vol.46 , pp. 346-353
    • Nielsen, R.1
  • 22
    • 0035108825 scopus 로고    scopus 로고
    • A novel method for estimating substitution rate variation among sites in a large dataset of homologous DNA sequences
    • Pesole, G., and C. Saccone. 2001. A novel method for estimating substitution rate variation among sites in a large dataset of homologous DNA sequences. Genetics 157:859-865.
    • (2001) Genetics , vol.157 , pp. 859-865
    • Pesole, G.1    Saccone, C.2
  • 23
    • 0030928378 scopus 로고    scopus 로고
    • Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • Rambaut, A., and N. C. Grassly. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 24
    • 0036205377 scopus 로고    scopus 로고
    • TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
    • Schmidt, H. A., K. Strimmer, M. Vingron, and A. von Haeseler. 2002. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504.
    • (2002) Bioinformatics , vol.18 , pp. 502-504
    • Schmidt, H.A.1    Strimmer, K.2    Vingron, M.3    Von Haeseler, A.4
  • 25
    • 0029836454 scopus 로고    scopus 로고
    • Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies
    • Strimmer, K., and A. von Haeseler. 1996. Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964-969.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 964-969
    • Strimmer, K.1    Von Haeseler, A.2
  • 26
    • 0001336205 scopus 로고    scopus 로고
    • Phylogenetic inference
    • D. M. Hillis, C. Moritz, and B. K. Mable, eds. Sinauer Associates, Sunderland, Mass
    • Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogenetic inference. Pp. 407-514 in D. M. Hillis, C. Moritz, and B. K. Mable, eds. Molecular systematics. Sinauer Associates, Sunderland, Mass.
    • (1996) Molecular Systematics , pp. 407-514
    • Swofford, D.L.1    Olsen, G.J.2    Waddell, P.J.3    Hillis, D.M.4
  • 27
    • 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
  • 28
    • 0002671410 scopus 로고
    • Some probabilistic and statistical problems in the analysis of DNA sequences
    • M. S. Waterman, ed. The American Mathematical Society, Providence, R.I.
    • Tavaré, S. 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. Pp. 57-86 in M. S. Waterman, ed. Some mathematical questions in biology: DNA sequence analysis. The American Mathematical Society, Providence, R.I.
    • (1986) Some Mathematical Questions in Biology: DNA Sequence Analysis , pp. 57-86
    • Tavaré, S.1
  • 29
    • 0034538854 scopus 로고    scopus 로고
    • An updated and comprehensive rRNA phylogeny of (crown) eukaryotes based on rate-calibrated evolutionary distances
    • Van de Peer, Y., S. L. Baldauf, W. F. Doolittle, and A. Meyer. 2000. An updated and comprehensive rRNA phylogeny of (crown) eukaryotes based on rate-calibrated evolutionary distances. J. Mol. Evol. 51:565-576.
    • (2000) J. Mol. Evol. , vol.51 , pp. 565-576
    • Van de Peer, Y.1    Baldauf, S.L.2    Doolittle, W.F.3    Meyer, A.4
  • 30
    • 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. D. Rijk, and R. D. 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    Rijk, P.D.3    Wachter, R.D.4
  • 31
    • 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
  • 32
    • 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. 10:1396-1401.
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 1396-1401
    • Yang, Z.1
  • 33
    • 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
  • 34
    • 0028813337 scopus 로고
    • A space-time process model for the evolution of DNA sequences
    • -. 1995. A space-time process model for the evolution of DNA sequences. Genetics 139:993-1005.
    • (1995) Genetics , vol.139 , pp. 993-1005
  • 35
    • 0030451420 scopus 로고    scopus 로고
    • Among-site rate variation and its impact on phylogenetic analyses
    • -. 1996. Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol. Evol. 11:367-372.
    • (1996) Trends Ecol. Evol. , vol.11 , pp. 367-372
  • 36
    • 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.