메뉴 건너뛰기




Volumn 38, Issue 3, 2006, Pages 848-857

Model type, implicit data weighting, and model averaging in phylogenetics

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; ARTICLE; BIOLOGICAL MODEL; PHYLOGENY; STATISTICAL MODEL; UNCERTAINTY;

EID: 33244473488     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2005.08.005     Document Type: Article
Times cited : (9)

References (30)
  • 1
    • 0000501656 scopus 로고
    • Information theory as an extension of the maximum likelihood principle
    • B.N. Petrov F. Csaki Akademiaai Kiado Budapest
    • H. Akaike Information theory as an extension of the maximum likelihood principle B.N. Petrov F. Csaki Second International Symposium on Information Theory 1973 Akademiaai Kiado Budapest 267 281
    • (1973) Second International Symposium on Information Theory , pp. 267-281
    • Akaike, H.1
  • 2
    • 4344651358 scopus 로고    scopus 로고
    • Phylogenetic relationships and biogeography of the desert plant genus Fagonia (Zygophyllaceae), inferred by parsimony and Bayesian model averaging
    • B.A. Beier, J.A.A. Nylander, M.W. Chase, and M. Thulin Phylogenetic relationships and biogeography of the desert plant genus Fagonia (Zygophyllaceae), inferred by parsimony and Bayesian model averaging Mol. Phylogenet. Evol. 33 2004 91 108
    • (2004) Mol. Phylogenet. Evol. , vol.33 , pp. 91-108
    • Beier, B.A.1    Nylander, J.A.A.2    Chase, M.W.3    Thulin, M.4
  • 3
    • 9944255059 scopus 로고    scopus 로고
    • Partitioned Bayesian analysis, partition choice, and the phylogenetic relationships of scincid lizards
    • M.C. Brandley, A. Schmitz, and T.W. Reeder Partitioned Bayesian analysis, partition choice, and the phylogenetic relationships of scincid lizards Syst. Biol. 54 2005 373 390
    • (2005) Syst. Biol. , vol.54 , pp. 373-390
    • Brandley, M.C.1    Schmitz, A.2    Reeder, T.W.3
  • 4
    • 0036005521 scopus 로고    scopus 로고
    • Combined data, bayesian Phylogenetics, and the origin of the New Zealand Cicada Genera
    • T.R. Buckley, P. Arensburger, C. Simon, and G.K. Chambers Combined data, bayesian Phylogenetics, and the origin of the New Zealand Cicada Genera Syst. Biol. 51 2002 4 18
    • (2002) Syst. Biol. , vol.51 , pp. 4-18
    • Buckley, T.R.1    Arensburger, P.2    Simon, C.3    Chambers, G.K.4
  • 8
    • 0043071131 scopus 로고    scopus 로고
    • Stability in phylogenetic formulations and its relationship to nodal support
    • G. Giribet Stability in phylogenetic formulations and its relationship to nodal support Syst. Biol. 52 2003 554 564
    • (2003) Syst. Biol. , vol.52 , pp. 554-564
    • Giribet, G.1
  • 9
    • 0038287878 scopus 로고    scopus 로고
    • Data exploration in phylogenetic inference: Scientific, heuristic, or neither
    • T. Grant, and A.G. Kluge Data exploration in phylogenetic inference: scientific, heuristic, or neither Cladistics 19 2003 379 418
    • (2003) Cladistics , vol.19 , pp. 379-418
    • Grant, T.1    Kluge, A.G.2
  • 10
    • 2442671519 scopus 로고    scopus 로고
    • Bayesian phylogenetic model selection using reversible jump markov chain Monte Carlo
    • J.P Huelsenbeck, B. Larget, and M.E. Alfaro Bayesian phylogenetic model selection using reversible jump markov chain Monte Carlo Mol. Biol. Evol. 21 2004 1123 1133
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1123-1133
    • Huelsenbeck, J.P.1    Larget, B.2    Alfaro, M.E.3
  • 11
    • 11144277878 scopus 로고    scopus 로고
    • Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models
    • J.P. Huelsenbeck, and B. Rannala Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models Syst. Biol. 53 2004 904 913
    • (2004) Syst. Biol. , vol.53 , pp. 904-913
    • Huelsenbeck, J.P.1    Rannala, B.2
  • 12
    • 0030732143 scopus 로고    scopus 로고
    • Majority-rule consensus of phylogenetic trees obtained by maximum-likelihood analysis
    • L.S. Jermiin, G.J. Olsen, K.L. Mengersen, and S. Easteal Majority-rule consensus of phylogenetic trees obtained by maximum-likelihood analysis Mol. Biol. Evol. 14 1997 1296 1302
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 1296-1302
    • Jermiin, L.S.1    Olsen, G.J.2    Mengersen, K.L.3    Easteal, S.4
  • 13
    • 0024307824 scopus 로고
    • Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order of Hominoidea
    • H. Kishino, and M. Hasegawa Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order of Hominoidea J. Mol. Evol. 29 1989 170 179
    • (1989) J. Mol. Evol. , vol.29 , pp. 170-179
    • Kishino, H.1    Hasegawa, M.2
  • 14
    • 2442581218 scopus 로고    scopus 로고
    • The importance of proper model assumption in Bayesian phylogenetics
    • A.R. Lemmon, and E.C. Moriarty The importance of proper model assumption in Bayesian phylogenetics Syst. Biol. 53 2004 265 277
    • (2004) Syst. Biol. , vol.53 , pp. 265-277
    • Lemmon, A.R.1    Moriarty, E.C.2
  • 15
    • 4644320044 scopus 로고    scopus 로고
    • Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamaders inferred from complete mitochondrial genomes
    • R.L. Mueller, R.J. Macey, M. Jaekel, D.B. Wake, and J. Boore Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamaders inferred from complete mitochondrial genomes Proc. Natl. Acad. Sci. USA 101 2004 13820 13825
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 13820-13825
    • Mueller, R.L.1    MacEy, R.J.2    Jaekel, M.3    Wake, D.B.4    Boore, J.5
  • 16
    • 9644301241 scopus 로고    scopus 로고
    • Model selection and model averaging in phylogenetics: Advantages of Akaike Information criterion and Bayesian approaches over likelihood ratio tests
    • D. Posada, and T.R. Buckley Model selection and model averaging in phylogenetics: advantages of Akaike Information criterion and Bayesian approaches over likelihood ratio tests Syst. Biol. 53 2004 793 808
    • (2004) Syst. Biol. , vol.53 , pp. 793-808
    • Posada, D.1    Buckley, T.R.2
  • 17
    • 0031773680 scopus 로고    scopus 로고
    • Modeltest: Testing the model of DNA substitution
    • D. Posada, and K. Crandall Modeltest: testing the model of DNA substitution Bioinformatics 14 1998 817 818
    • (1998) Bioinformatics , vol.14 , pp. 817-818
    • Posada, D.1    Crandall, K.2
  • 18
    • 0035527410 scopus 로고    scopus 로고
    • Selecting the best-fit model of nucleotide substitution
    • D. Posada, and K. Crandall Selecting the best-fit model of nucleotide substitution Syst. Biol. 50 2001 580 601
    • (2001) Syst. Biol. , vol.50 , pp. 580-601
    • Posada, D.1    Crandall, K.2
  • 20
    • 0034350371 scopus 로고    scopus 로고
    • Is there a justification for differential a priori weighting in coding sequences. a case study from rbcL and Apocynaceae s.l
    • B. Sennblad, and B. Bremer Is there a justification for differential a priori weighting in coding sequences. A case study from rbcL and Apocynaceae s.l Syst. Biol. 49 2000 101 113
    • (2000) Syst. Biol. , vol.49 , pp. 101-113
    • Sennblad, B.1    Bremer, B.2
  • 21
    • 15444373349 scopus 로고    scopus 로고
    • Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data
    • T.-K. Seo, H. Kishino, and J.L. Thorne Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data Proc. Natl. Acad. Sci. USA 102 2005 4436 4441
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 4436-4441
    • Seo, T.-K.1    Kishino, H.2    Thorne, J.L.3
  • 22
    • 0032766857 scopus 로고    scopus 로고
    • Multiple comparisons of log-likelihoods with applications to phylogenetic inference
    • H. Shimodaira, and M. Hasegawa Multiple comparisons of log-likelihoods with applications to phylogenetic inference Mol. Biol. Evol. 16 1999 1114 1116
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1114-1116
    • Shimodaira, H.1    Hasegawa, M.2
  • 23
    • 0036038036 scopus 로고    scopus 로고
    • Snake phylogeny: Evidence from nuclear and mitochondrial genes
    • J.B. Slowinski, and R.L. Lawson Snake phylogeny: evidence from nuclear and mitochondrial genes Mol. Phylogenet. Evol. 24 2002 194 202
    • (2002) Mol. Phylogenet. Evol. , vol.24 , pp. 194-202
    • Slowinski, J.B.1    Lawson, R.L.2
  • 24
    • 4644295677 scopus 로고    scopus 로고
    • The contest between parsimony and likelihood
    • E. Sober The contest between parsimony and likelihood Syst. Biol. 53 2004 644 653
    • (2004) Syst. Biol. , vol.53 , pp. 644-653
    • Sober, E.1
  • 25
    • 41049111540 scopus 로고    scopus 로고
    • Inferring confidence sets of possibly misspecified gene trees
    • K. Strimmer, and A. Rambaut Inferring confidence sets of possibly misspecified gene trees Proc. Roy. Soc. Lond. B 269 2002 137 142
    • (2002) Proc. Roy. Soc. Lond. B , vol.269 , pp. 137-142
    • Strimmer, K.1    Rambaut, A.2
  • 26
    • 33244465943 scopus 로고
    • Further analysis of the data by Akaike's information criterion of model fitting
    • N. Sugiura Further analysis of the data by Akaike's information criterion of model fitting Suri-Kagaku (Mathematic Sciences) 153 1978 12 18 in Japanese
    • (1978) Suri-Kagaku (Mathematic Sciences) , vol.153 , pp. 12-18
    • Sugiura, N.1
  • 28
    • 0034350323 scopus 로고    scopus 로고
    • Phylogenetic relationships among the Phrynosomatid Sand Lizards inferred from mitochondrial DNA sequences generated by heterogeneous evolutionary processes
    • J. Wilgenbusch, and K. De Queiroz Phylogenetic relationships among the Phrynosomatid Sand Lizards inferred from mitochondrial DNA sequences generated by heterogeneous evolutionary processes Syst. Biol. 49 2000 592 612
    • (2000) Syst. Biol. , vol.49 , pp. 592-612
    • Wilgenbusch, J.1    De Queiroz, K.2
  • 29
    • 0036431235 scopus 로고    scopus 로고
    • Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support
    • T.P. Wilcox, D.J. Zwicki, T.A. Heath, and D.M. Hillis Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support Mol. Phylogenet. Evol. 25 2002 361 371
    • (2002) Mol. Phylogenet. Evol. , vol.25 , pp. 361-371
    • Wilcox, T.P.1    Zwicki, D.J.2    Heath, T.A.3    Hillis, D.M.4
  • 30
    • 0029970097 scopus 로고    scopus 로고
    • Maximum-likelihood models for combined analyses of multiple sequence data
    • Z. Yang Maximum-likelihood models for combined analyses of multiple sequence data J. Mol. Evol. 42 1996 587 596
    • (1996) J. Mol. Evol. , vol.42 , pp. 587-596
    • Yang, Z.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.