메뉴 건너뛰기




Volumn 53, Issue 4, 2004, Pages 571-581

A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data

Author keywords

Bayesian inference; MCMC; Mixture model; Phylogeny; Rate heterogeneity; Secondary structure; Sequence evolution

Indexed keywords

RIBOSOME RNA; RNA, RIBOSOMAL, 12S;

EID: 4243140058     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150490468675     Document Type: Article
Times cited : (410)

References (33)
  • 1
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein, J. P. 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.P.1
  • 3
    • 84972511893 scopus 로고
    • Practical Markov chain Monte Carlo
    • Geyer, C. J. 1992. Practical Markov chain Monte Carlo. Stat. Sci. 7:473-511.
    • (1992) Stat. Sci. , vol.7 , pp. 473-511
    • Geyer, C.J.1
  • 4
    • 0002517089 scopus 로고    scopus 로고
    • Introducing Markov chain Monte Carlo
    • (W. R. Gilks, S. Richardson, and D. J. Spiegelhalter, eds). Chapman and Hall, London
    • Gilks, W. R., S. Richardson, and D. J. Spiegelhalter. 1996. Introducing Markov chain Monte Carlo. Pages 1-19 in Markov chain Monte Carlo in practice (W. R. Gilks, S. Richardson, and D. J. Spiegelhalter, eds). Chapman and Hall, London.
    • (1996) Markov Chain Monte Carlo in Practice , pp. 1-19
    • Gilks, W.R.1    Richardson, S.2    Spiegelhalter, D.J.3
  • 5
    • 0030034071 scopus 로고    scopus 로고
    • Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA
    • Hickson, R. E., C. Simon, A. Cooper, G. S. Spicer, J. Sullivan, and D. Penny. 1996. Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA. Mol. Biol. Evol. 13:150-169.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 150-169
    • Hickson, R.E.1    Simon, C.2    Cooper, A.3    Spicer, G.S.4    Sullivan, J.5    Penny, D.6
  • 6
    • 4243559860 scopus 로고    scopus 로고
    • Compensatory neutral mutations and the evolution of RNA
    • Higgs, P. G. 1998. Compensatory neutral mutations and the evolution of RNA. Genetica 102:91-101.
    • (1998) Genetica , vol.102 , pp. 91-101
    • Higgs, P.G.1
  • 7
    • 0026300584 scopus 로고
    • Ribosomal DNA: Molecular evolution and phylogenetic inference
    • Hillis, D. M., and M. T. Dixon. 1991. Ribosomal DNA: Molecular evolution and phylogenetic inference. Q. Rev. Biol. 66:411-453.
    • (1991) Q. Rev. Biol. , vol.66 , pp. 411-453
    • Hillis, D.M.1    Dixon, M.T.2
  • 8
    • 0032923454 scopus 로고    scopus 로고
    • Variation in the pattern of nucleotide substitution across sites
    • Huelsenbeck, J. P., and Nielsen, R. 1999. Variation in the pattern of nucleotide substitution across sites. J. Mol. Evol. 48:86-93.
    • (1999) J. Mol. Evol. , vol.48 , pp. 86-93
    • Huelsenbeck, J.P.1    Nielsen, R.2
  • 9
    • 0035861456 scopus 로고    scopus 로고
    • Bayesian inference of phylogeny and its impact on evolutionary biology
    • Huelsenbeck, J. P., F. Ronquist, R. Nielsen, and J.P. Bollback. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-2314.
    • (2001) Science , vol.294 , pp. 2310-2314
    • Huelsenbeck, J.P.1    Ronquist, F.2    Nielsen, R.3    Bollback, J.P.4
  • 10
    • 0036728808 scopus 로고    scopus 로고
    • Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution
    • Jow, H., C. Hudelot, M. Rattray, and P. G. Higgs. 2002. Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution. Mol. Biol. Evol. 19:1591-1601.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 1591-1601
    • Jow, H.1    Hudelot, C.2    Rattray, M.3    Higgs, P.G.4
  • 11
    • 0032529584 scopus 로고    scopus 로고
    • Models of natural mutations including site heterogeneity
    • Koshi, J. M., and R. A. Goldstein. 1998. Models of natural mutations including site heterogeneity. Proteins: Struct. Funct. Genet. 32:289-295.
    • (1998) Proteins: Struct. Funct. Genet. , vol.32 , pp. 289-295
    • Koshi, J.M.1    Goldstein, R.A.2
  • 12
    • 0033219088 scopus 로고    scopus 로고
    • Dynamically heterogeneous partitions and phylogenetic inference: An evaluation of analytical strategies with cytochrome b and ND6 gene sequences in cranes
    • Krajewski, C., M. G. Fain, L. Buckley, and D. G. King. 1999. Dynamically heterogeneous partitions and phylogenetic inference: An evaluation of analytical strategies with cytochrome b and ND6 gene sequences in cranes. Mol. Phylo. Evol. 13:302-313.
    • (1999) Mol. Phylo. Evol. , vol.13 , pp. 302-313
    • Krajewski, C.1    Fain, M.G.2    Buckley, L.3    King, D.G.4
  • 13
    • 0032976397 scopus 로고    scopus 로고
    • Markov chain monte carlo algorithms for the Bayesian analysis of phylogenetic trees
    • Larget, B., and D. L. Simon. 1999. Markov chain monte carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16:750-759.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 750-759
    • Larget, B.1    Simon, D.L.2
  • 14
    • 2442691520 scopus 로고    scopus 로고
    • A Bayesian mixture model for across site heterogeneities in the amino-acid replacement process
    • in press
    • Lartillot, N., and H. Philippe. 2004. A Bayesian mixture model for across site heterogeneities in the amino-acid replacement process. Mol. Biol. Evol. in press.
    • (2004) Mol. Biol. Evol.
    • Lartillot, N.1    Philippe, H.2
  • 15
    • 0035527396 scopus 로고    scopus 로고
    • A likelihood approach to estimating phylogeny from discrete morphological character data
    • Lewis, P. O. 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 50:913-925.
    • (2001) Syst. Biol. , vol.50 , pp. 913-925
    • Lewis, P.O.1
  • 16
    • 0035927638 scopus 로고    scopus 로고
    • Major fungal lineages derived from lichen-symbiotic ancestors
    • Lutzoni, F., M. Pagel, and V. Reeb. 2001. Major fungal lineages derived from lichen-symbiotic ancestors. Nature 411:937-940.
    • (2001) Nature , vol.411 , pp. 937-940
    • Lutzoni, F.1    Pagel, M.2    Reeb, V.3
  • 17
    • 0034350422 scopus 로고    scopus 로고
    • More taxa or more characters revisted: Combining data from nuclear protein-coding genes for phylogenetic analyzes of Noctuoidea (Insecta: Lepidoptera)
    • Mitchell, A., C., Mitter, and J.C. Regier. 2000. More taxa or more characters revisted: Combining data from nuclear protein-coding genes for phylogenetic analyzes of Noctuoidea (Insecta: Lepidoptera). Syst. Biol. 49:202-224.
    • (2000) Syst. Biol. , vol.49 , pp. 202-224
    • Mitchell, A.1    Mitter, C.2    Regier, J.C.3
  • 19
    • 0028097770 scopus 로고
    • Detecting correlated evolution on phylogenies: A general method for the comparative analysis of discrete characters
    • Pagel, M. 1994. Detecting correlated evolution on phylogenies: A general method for the comparative analysis of discrete characters. Proc. R. Soc. B 255:37-45.
    • (1994) Proc. R. Soc. B , vol.255 , pp. 37-45
    • Pagel, M.1
  • 20
    • 0033613376 scopus 로고    scopus 로고
    • Inferring the historical patterns of biological evolution
    • Pagel, M. 1999. Inferring the historical patterns of biological evolution. Nature 401:877-884.
    • (1999) Nature , vol.401 , pp. 877-884
    • Pagel, M.1
  • 21
    • 0000176247 scopus 로고    scopus 로고
    • Accounting for phylogenetic uncertainty in comparative studies of evolution and adaptation
    • (M. Lässig and A. Valleriani, eds.). Springer-Verlag, Berlin
    • Pagel, M., and F. Lutzoni. 2002. Accounting for phylogenetic uncertainty in comparative studies of evolution and adaptation. Pages 148-161 in Biological evolution and statistical physics (M. Lässig and A. Valleriani, eds.). Springer-Verlag, Berlin.
    • (2002) Biological Evolution and Statistical Physics , pp. 148-161
    • Pagel, M.1    Lutzoni, F.2
  • 22
    • 0035527410 scopus 로고    scopus 로고
    • Selecting the best fit model of nucleotide substitution
    • Posada, D., and K. A. Crandall. 2001. Selecting the best fit model of nucleotide substitution. Syst. Biol. 50:580-601.
    • (2001) Syst. Biol. , vol.50 , pp. 580-601
    • Posada, D.1    Crandall, K.A.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
    • 0000783674 scopus 로고    scopus 로고
    • Hypothesis testing and model selection
    • (W. R. Gilks, S. Richardson, and D. J. Spiegelhalter, eds.). Chapman and Hall, London
    • Raftery, A. E. 1996. Hypothesis testing and model selection. Pages 163-188 in Markov chain Monte Carlo in practice (W. R. Gilks, S. Richardson, and D. J. Spiegelhalter, eds.). Chapman and Hall, London.
    • (1996) Markov Chain Monte Carlo in Practice , pp. 163-188
    • Raftery, A.E.1
  • 25
    • 0242365676 scopus 로고    scopus 로고
    • Genome-scale approaches to resolving incongruence in molecular phylogenies
    • Rokas, A., B. L. Williams, N. King, and S. B. Carroll. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804.
    • (2003) Nature , vol.425 , pp. 798-804
    • Rokas, A.1    Williams, B.L.2    King, N.3    Carroll, S.B.4
  • 26
    • 0035156561 scopus 로고    scopus 로고
    • RNA sequence evolution with secondary structure constraints: Comparison of substitution rate models using maximum likelihood methods
    • Savill, N. J., D. C. Hoyle, and P. G. Higgs. 2001. RNA sequence evolution with secondary structure constraints: Comparison of substitution rate models using maximum likelihood methods. Genetics 157:399-411.
    • (2001) Genetics , vol.157 , pp. 399-411
    • Savill, N.J.1    Hoyle, D.C.2    Higgs, P.G.3
  • 27
    • 0028512129 scopus 로고
    • A stochastic model for the evolution of autocorrelated DNA sequences
    • Schöniger, M., and von A. Haeseler. 1994. A stochastic model for the evolution of autocorrelated DNA sequences. Mol. Phylo. Evol. 3:240-247.
    • (1994) Mol. Phylo. Evol. , vol.3 , pp. 240-247
    • Schöniger, M.1    Von Haeseler, A.2
  • 28
    • 0028251187 scopus 로고
    • Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers
    • Simon, C., F. Frati, A. Beckenbach, B. Crespi, H. Liu, and P. Flook. 1994. Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann. Entomol. Soc. Am. 87:651-701.
    • (1994) Ann. Entomol. Soc. Am. , vol.87 , pp. 651-701
    • Simon, C.1    Frati, F.2    Beckenbach, A.3    Crespi, B.4    Liu, H.5    Flook, P.6
  • 29
    • 0029815120 scopus 로고    scopus 로고
    • Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules
    • Springer, M. S., and E. Douzery. 1996. Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules. J. Mol. Evol. 43:357-373.
    • (1996) J. Mol. Evol. , vol.43 , pp. 357-373
    • Springer, M.S.1    Douzery, E.2
  • 30
    • 0001336205 scopus 로고    scopus 로고
    • Phylogenetic inference
    • (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer, Sunderland, Massachusetts
    • Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogenetic inference. Pages 407-514 in Molecular systematics, 2nd edition (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer, Sunderland, Massachusetts.
    • (1996) Molecular Systematics, 2nd Edition , pp. 407-514
    • Swofford, D.L.1    Olsen, G.J.2    Waddell, P.J.3    Hillis, D.M.4
  • 31
    • 0031669749 scopus 로고    scopus 로고
    • Genealogical inference from microsatellite data
    • Wilson, I., and D. Balding. 1998. Genealogical inference from microsatellite data. Genetics 150:499-510.
    • (1998) Genetics , vol.150 , pp. 499-510
    • Wilson, I.1    Balding, D.2
  • 32
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • Yang, Z. 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
    • Yang, Z.1
  • 33
    • 0034097381 scopus 로고    scopus 로고
    • Codon-substitution models for heterogeneous selection pressure at amino acid sites
    • Yang, Z., R., Nielsen, N., Goldman, and A.-M. K. Pedersen. 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.K.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.