메뉴 건너뛰기




Volumn 21, Issue 7, 2004, Pages 1401-1408

Genome phylogenetic analysis based on extended gene contents

Author keywords

Additive genome distance; Comparative genomics; Gene content; Phylogenetic inference

Indexed keywords

ARTICLE; BACTERIAL GENOME; COMPUTER SIMULATION; EVOLUTION; GENE CONTENT; GENE DUPLICATION; GENETIC DISTANCE; GENOME; MULTIGENE FAMILY; PHYLOGENETIC TREE CONSTRUCTION METHOD; PHYLOGENY; STOCHASTIC MODEL;

EID: 3042643735     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msh138     Document Type: Article
Times cited : (47)

References (37)
  • 1
    • 0037329391 scopus 로고    scopus 로고
    • Bayes or Bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and boot-strapping in assessing phylogenetic confidence
    • Alfaro, M. E., S. Zoller, and F. Lutzoni. 2003. Bayes or Bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and boot-strapping in assessing phylogenetic confidence. Mol. Biol. Evol. 20:255-266.
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 255-266
    • Alfaro, M.E.1    Zoller, S.2    Lutzoni, F.3
  • 2
    • 0034633626 scopus 로고    scopus 로고
    • Lineage-specific loss and divergence of functionally linked genes in eukaryotes
    • Aravind, L., H. Watanabe, D. J. Lipman, and E. V. Koonin. 2000. Lineage-specific loss and divergence of functionally linked genes in eukaryotes. Proc. Natl. Acad. Sci. USA 97:11319-11324.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 11319-11324
    • Aravind, L.1    Watanabe, H.2    Lipman, D.J.3    Koonin, E.V.4
  • 3
    • 0036210883 scopus 로고    scopus 로고
    • Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores
    • Clarke, G. D. P., R. G. Beiko, M. A. Ragan, and R. L. Charlebois. 2002. Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. J. Bacteriol. 184:2072-2080.
    • (2002) J. Bacteriol. , vol.184 , pp. 2072-2080
    • Clarke, G.D.P.1    Beiko, R.G.2    Ragan, M.A.3    Charlebois, R.L.4
  • 4
    • 0042027842 scopus 로고    scopus 로고
    • Phylogenetics and the cohesion of bacterial genomes
    • Daubin, V., N. A. Moran, and H. Ochman. 2003. Phylogenetics and the cohesion of bacterial genomes. Science 301:829-832.
    • (2003) Science , vol.301 , pp. 829-832
    • Daubin, V.1    Moran, N.A.2    Ochman, H.3
  • 5
    • 0033603539 scopus 로고    scopus 로고
    • Phylogenetic classification and the universal tree
    • Doolittle, W. F. 1999a. Phylogenetic classification and the universal tree. Science 284:2124-2129.
    • (1999) Science , vol.284 , pp. 2124-2129
    • Doolittle, W.F.1
  • 6
    • 0000298267 scopus 로고    scopus 로고
    • Technical comments (Response) on Doolittle (1999a)
    • Doolittle, W. F. 1999b. Technical comments (Response) on Doolittle (1999a). Science 286:1443a.
    • (1999) Science , vol.286
    • Doolittle, W.F.1
  • 7
    • 0032510454 scopus 로고    scopus 로고
    • Archaeal genomics: Do Archaea have a mixed heritage?
    • Doolittle, W. F., and J. M. Logsdon. 1998. Archaeal genomics: do Archaea have a mixed heritage? Curr. Biol. 8:R209-R211.
    • (1998) Curr. Biol. , vol.8
    • Doolittle, W.F.1    Logsdon, J.M.2
  • 8
    • 0033669672 scopus 로고    scopus 로고
    • Horizontal gene transfer among microbial genomes: New insights from complete genome analysis
    • Eisen, J. A. 2000. Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Curr. Opin. Genet. Dev. 10:606-611.
    • (2000) Curr. Opin. Genet. Dev. , vol.10 , pp. 606-611
    • Eisen, J.A.1
  • 9
    • 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
  • 10
    • 0033231209 scopus 로고    scopus 로고
    • Whole genome-based phylogenetic analysis of free-living microorganisms
    • Fitz-Gibbon, S. T., and C. H. House. 1999. Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res. 27:4218-4222.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 4218-4222
    • Fitz-Gibbon, S.T.1    House, C.H.2
  • 11
    • 0028888465 scopus 로고
    • Protein-based phylogenies support a chimeric origin for the eukaryotic genome
    • Golding, G. B., and R. S. Gupta. 1995. Protein-based phylogenies support a chimeric origin for the eukaryotic genome. Mol. Biol. Evol. 12:1-6.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 1-6
    • Golding, G.B.1    Gupta, R.S.2
  • 12
    • 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
  • 13
    • 0032728408 scopus 로고    scopus 로고
    • Statistical methods for testing functional divergence after gene duplication
    • Gu, X. 1999. Statistical methods for testing functional divergence after gene duplication. Mol. Biol. Evol. 16:1664-1674.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1664-1674
    • Gu, X.1
  • 14
    • 0002984215 scopus 로고    scopus 로고
    • A simple evolutionary model for genome phylogeny inference based on gene content
    • D. Sankoff and J. H. Nadeau, eds. Kluwer Academic Publishers, Dordrect, The Netherlands
    • Gu, X. 2000. A simple evolutionary model for genome phylogeny inference based on gene content. Pp. 515-524 in D. Sankoff and J. H. Nadeau, eds. Comparative genomics. Kluwer Academic Publishers, Dordrect, The Netherlands.
    • (2000) Comparative Genomics , pp. 515-524
    • Gu, X.1
  • 15
    • 0035061686 scopus 로고    scopus 로고
    • Maximum likelihood approach for gene family evolution under functional divergence
    • Gu, X. 2001. Maximum likelihood approach for gene family evolution under functional divergence. Mol. Biol. Evol. 18:453-464.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 453-464
    • Gu, X.1
  • 16
    • 0036141943 scopus 로고    scopus 로고
    • Testing the parsimony test of genome duplications: A counterexample
    • Gu, X., and W. Huang. 2002. Testing the parsimony test of genome duplications: a counterexample. Genome Res. 12:1-2.
    • (2002) Genome Res. , vol.12 , pp. 1-2
    • Gu, X.1    Huang, W.2
  • 17
    • 0036613509 scopus 로고    scopus 로고
    • Age-distribution of human gene families showing equal roles of large and small-scale duplications in vertebrate evolution
    • Gu, X., Y. Wang, and J. Gu. 2002. Age-distribution of human gene families showing equal roles of large and small-scale duplications in vertebrate evolution. Nature Genet. 31: 205-209.
    • (2002) Nature Genet. , vol.31 , pp. 205-209
    • Gu, X.1    Wang, Y.2    Gu, J.3
  • 18
    • 0036218557 scopus 로고    scopus 로고
    • Using homolog groups to create a whole-genomic tree of free-living organisms: An update
    • House, C. H., and S. T. Fitz-Gibbon. 2002. Using homolog groups to create a whole-genomic tree of free-living organisms: an update. J. Mol. Evol. 54:539-547.
    • (2002) J. Mol. Evol. , vol.54 , pp. 539-547
    • House, C.H.1    Fitz-Gibbon, S.T.2
  • 19
    • 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
  • 20
    • 0000298267 scopus 로고    scopus 로고
    • Technical comments on Doolittle [1999a]
    • Huynen, M. A., B. Snel, and P. Bork. 1999. Technical comments on Doolittle [1999a]. Science 286:1443a.
    • (1999) Science , vol.286
    • Huynen, M.A.1    Snel, B.2    Bork, P.3
  • 21
    • 0033940941 scopus 로고    scopus 로고
    • Gene and context: Integrative approaches to genome analysis
    • Huynen, M. A., and B. Snel. 2000. Gene and context: integrative approaches to genome analysis. Adv. Prot. Chem. 54:345-379.
    • (2000) Adv. Prot. Chem. , vol.54 , pp. 345-379
    • Huynen, M.A.1    Snel, B.2
  • 22
    • 0035046878 scopus 로고    scopus 로고
    • Lineage-specific gene expansions in bacterial and archaeal genomes
    • Jordan, I. K., K. S. Makarova, J. L. Spouge, Y. I. Wolf, and E. V. Koonin. 2001. Lineage-specific gene expansions in bacterial and archaeal genomes. Genome Res. 11:555-565.
    • (2001) Genome Res. , vol.11 , pp. 555-565
    • Jordan, I.K.1    Makarova, K.S.2    Spouge, J.L.3    Wolf, Y.I.4    Koonin, E.V.5
  • 23
    • 0036499057 scopus 로고    scopus 로고
    • SHOT: A Web server for the construction of genome phylogenies
    • Korbel, J. O., B. Snel, M. A. Huynen, and P. Bork. 2002. SHOT: a Web server for the construction of genome phylogenies. Trends Genet. 18:158-62.
    • (2002) Trends Genet. , vol.18 , pp. 158-162
    • Korbel, J.O.1    Snel, B.2    Huynen, M.A.3    Bork, P.4
  • 24
    • 0032482924 scopus 로고    scopus 로고
    • Molecular archaeology of the Escherichia coli genome
    • Lawrence, J. G., and H. Ochman. 1998. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA 95:9413-9417.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 9413-9417
    • Lawrence, J.G.1    Ochman, H.2
  • 25
    • 0033918311 scopus 로고    scopus 로고
    • Whole-genome trees based on the occurrence of folds and orthologs: Implications for comparing genomes on different levels
    • Lin, J., and M. Gerstein. 2000. Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. Genome Res. 10:808-818.
    • (2000) Genome Res. , vol.10 , pp. 808-818
    • Lin, J.1    Gerstein, M.2
  • 26
    • 0034572821 scopus 로고    scopus 로고
    • Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs)
    • RESEARCH0009
    • Natale, D. A., U. T. Shankavaram, M. Y. Galperin, Y. I. Wolf, L. Aravind, and E. V. Koonin. 2000. Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs). Genome Biol. 1, RESEARCH0009.
    • (2000) Genome Biol. , vol.1
    • Natale, D.A.1    Shankavaram, U.T.2    Galperin, M.Y.3    Wolf, Y.I.4    Aravind, L.5    Koonin, E.V.6
  • 27
    • 0030791307 scopus 로고    scopus 로고
    • Evolution by the birth-and-death process in multigene families of the vertebrate immune system
    • Nei, M., X. Gu, and R. Sitnikova. 1997. Evolution by the birth-and-death process in multigene families of the vertebrate immune system. Proc. Natl. Acad. Sci. USA 94:7799-7806.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 7799-7806
    • Nei, M.1    Gu, X.2    Sitnikova, R.3
  • 28
    • 0033609333 scopus 로고    scopus 로고
    • Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima
    • Nelson, K. E., R. A. Clayton, S. R. Gill, et al. (29 co-authors). 1999. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 339:323-329.
    • (1999) Nature , vol.339 , pp. 323-329
    • Nelson, K.E.1    Clayton, R.A.2    Gill, S.R.3
  • 29
    • 0028055018 scopus 로고
    • The winds of (evolutionary) change: Breathing new life into microbiology
    • Olsen, G. J., C. R. Woese, and R. Overbeek. 1994. The winds of (evolutionary) change: breathing new life into microbiology. J. Bacteriol. 176:1-6.
    • (1994) J. Bacteriol. , vol.176 , pp. 1-6
    • Olsen, G.J.1    Woese, C.R.2    Overbeek, R.3
  • 31
    • 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
  • 32
    • 0035546156 scopus 로고    scopus 로고
    • Gene and genome duplication
    • Sankoff, D. 2001. Gene and genome duplication. Curr. Opin. Genet. Dev. 11:681-684.
    • (2001) Curr. Opin. Genet. Dev. , vol.11 , pp. 681-684
    • Sankoff, D.1
  • 33
    • 0032900532 scopus 로고    scopus 로고
    • Genome phylogeny based on gene content
    • Snel, B., P. Bork, and M. A. Huynen. 1999. Genome phylogeny based on gene content. Nat. Genet. 21:108-110.
    • (1999) Nat. Genet. , vol.21 , pp. 108-110
    • Snel, B.1    Bork, P.2    Huynen, M.A.3
  • 34
    • 0037058983 scopus 로고    scopus 로고
    • Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics
    • Suzuki, Y., G. V. Glazko, and M. Nei. 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. USA 99:16138-16143.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 16138-16143
    • Suzuki, Y.1    Glazko, G.V.2    Nei, M.3
  • 35
    • 0032778047 scopus 로고    scopus 로고
    • The genomic tree as revealed from whole proteome comparisons
    • Tekaia, F., A. Lazcano, and B. Dujon. 1999. The genomic tree as revealed from whole proteome comparisons. Genome Res. 9:550-557.
    • (1999) Genome Res. , vol.9 , pp. 550-557
    • Tekaia, F.1    Lazcano, A.2    Dujon, B.3
  • 36
    • 0032499698 scopus 로고    scopus 로고
    • The universal ancestor
    • Woese, C. 1998. The universal ancestor. Proc. Natl. Acad. Sci. USA 95:6854-6859.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 6854-6859
    • Woese, C.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.