메뉴 건너뛰기




Volumn 10, Issue 1, 2010, Pages

On the artefactual parasitic eubacteria clan in conditioned logdet phylogenies: Heterotachy and ortholog identification artefacts as explanations

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIUM; DATABASE; ENDOSYMBIONT; ESTIMATION METHOD; GENE; PARASITE; PHYLOGENETICS;

EID: 78649505234     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-10-343     Document Type: Article
Times cited : (5)

References (42)
  • 1
    • 3042595153 scopus 로고    scopus 로고
    • Patterns of bacterial gene movement
    • 10.1093/molbev/msh129. 15115802
    • Patterns of bacterial gene movement. W Hao BG Golding, Mol Biol Evol 2004 21 7 1294 1307 10.1093/molbev/msh129 15115802
    • (2004) Mol Biol Evol , vol.21 , Issue.7 , pp. 1294-1307
    • Hao, W.1    Golding, B.G.2
  • 2
    • 27144493223 scopus 로고    scopus 로고
    • Genome trees and the nature of genome evolution
    • 10.1146/annurev.micro.59.030804.121233. 16153168
    • Genome trees and the nature of genome evolution. B Snel MA Huynen BE Dutilh, Annu Rev Microbiol 2005 59 191 209 10.1146/annurev.micro.59.030804. 121233 16153168
    • (2005) Annu Rev Microbiol , vol.59 , pp. 191-209
    • Snel, B.1    Huynen, M.A.2    Dutilh, B.E.3
  • 3
    • 34547830869 scopus 로고    scopus 로고
    • Reconstruction of highly heterogeneous gene-content evolution across the three domains of life
    • 10.1093/bioinformatics/btm165. 17646301
    • Reconstruction of highly heterogeneous gene-content evolution across the three domains of life. W Iwasaki T Takagi, Bioinformatics 2007 23 13 230 239 10.1093/bioinformatics/btm165 17646301
    • (2007) Bioinformatics , vol.23 , Issue.13 , pp. 9230-239
    • Iwasaki, W.1    Takagi, T.2
  • 4
    • 0036499057 scopus 로고    scopus 로고
    • SHOT: A web server for the construction of genome phylogenies
    • 10.1016/S0168-9525(01)02597-5. 11858840
    • SHOT: a web server for the construction of genome phylogenies. JO Korbel B Snel MA Huynen P Bork, Trends Genet 2002 18 3 158 162 10.1016/S0168-9525(01) 02597-5 11858840
    • (2002) Trends Genet , vol.18 , Issue.3 , pp. 158-162
    • Korbel, J.O.1    Snel, B.2    Huynen, M.A.3    Bork, P.4
  • 5
    • 33847312769 scopus 로고    scopus 로고
    • Conditioned genome reconstruction: How to avoid choosing the conditioning genome
    • 10.1080/10635150601156313. 17366135
    • Conditioned genome reconstruction: how to avoid choosing the conditioning genome. M Spencer D Bryant E Susko, Syst Biol 2007 56 1 25 43 10.1080/10635150601156313 17366135
    • (2007) Syst Biol , vol.56 , Issue.1 , pp. 25-43
    • Spencer, M.1    Bryant, D.2    Susko, E.3
  • 6
    • 0028361182 scopus 로고
    • Recovering evolutionary trees under a more realistic model of sequence evolution
    • 19391266
    • Recovering evolutionary trees under a more realistic model of sequence evolution. PJ Lockhart MA Steel MD Hendy D Penny, Mol Biol Evol 1994 11 4 605 612 19391266
    • (1994) Mol Biol Evol , vol.11 , Issue.4 , pp. 605-612
    • Lockhart, P.J.1    Steel, M.A.2    Hendy, M.D.3    Penny, D.4
  • 7
    • 1842505237 scopus 로고    scopus 로고
    • Deriving the genomic tree of life in the presence of horizontal gene transfer: conditioned reconstruction
    • 10.1093/molbev/msh061. 14739244
    • Deriving the genomic tree of life in the presence of horizontal gene transfer: conditioned reconstruction. JA Lake MC Rivera, Mol Biol Evol 2004 21 4 681 690 10.1093/molbev/msh061 14739244
    • (2004) Mol Biol Evol , vol.21 , Issue.4 , pp. 681-690
    • Lake, J.A.1    Rivera, M.C.2
  • 8
    • 13844306928 scopus 로고    scopus 로고
    • New methods ring changes for the tree of life
    • 10.1016/j.tree.2005.01.007. 16701350
    • New methods ring changes for the tree of life. JO McInerney M Wilkinson, Trends Ecol Evol 2005 20 3 105 107 10.1016/j.tree.2005.01.007 16701350
    • (2005) Trends Ecol Evol , vol.20 , Issue.3 , pp. 105-107
    • McInerney, J.O.1    Wilkinson, M.2
  • 9
    • 34247180015 scopus 로고    scopus 로고
    • The origin of eukaryotes: A reappraisal
    • 10.1038/nrg2071. 17429433
    • The origin of eukaryotes: a reappraisal. C de Duve, Nat Rev Genet 2007 8 5 395 403 10.1038/nrg2071 17429433
    • (2007) Nat Rev Genet , vol.8 , Issue.5 , pp. 395-403
    • De Duve, C.1
  • 10
    • 33646726959 scopus 로고    scopus 로고
    • Genomics and the irreducible nature of eukaryote cells
    • 10.1126/science.1121674. 16709776
    • Genomics and the irreducible nature of eukaryote cells. CG Kurland LJ Collins D Penny, Science 2006 312 5776 1011 1014 10.1126/science.1121674 16709776
    • (2006) Science , vol.312 , Issue.5776 , pp. 1011-1014
    • Kurland, C.G.1    Collins, L.J.2    Penny, D.3
  • 11
    • 20344361920 scopus 로고    scopus 로고
    • Does the 'Ring of Life' ring true?
    • 10.1016/j.tim.2005.03.012. 15936656
    • Does the 'Ring of Life' ring true? E Bapteste DA Walsh, Trends Microbiol 2005 13 6 256 261 10.1016/j.tim.2005.03.012 15936656
    • (2005) Trends Microbiol , vol.13 , Issue.6 , pp. 256-261
    • Bapteste, E.1    Walsh, D.A.2
  • 12
    • 17744394753 scopus 로고    scopus 로고
    • Phylogenomics and the reconstruction of the tree of life
    • 10.1038/nrg1603. 15861208
    • Phylogenomics and the reconstruction of the tree of life. F Delsuc H Brinkmann H Philippe, Nat Rev Genet 2005 6 5 361 375 10.1038/nrg1603 15861208
    • (2005) Nat Rev Genet , vol.6 , Issue.5 , pp. 361-375
    • Delsuc, F.1    Brinkmann, H.2    Philippe, H.3
  • 13
    • 4544313053 scopus 로고    scopus 로고
    • The ring of life provides evidence for a genome fusion origin of eukaryotes
    • 10.1038/nature02848. 15356622
    • The ring of life provides evidence for a genome fusion origin of eukaryotes. MC Rivera JA Lake, Nature 2004 431 7005 152 155 10.1038/nature02848 15356622
    • (2004) Nature , vol.431 , Issue.7005 , pp. 152-155
    • Rivera, M.C.1    Lake, J.A.2
  • 14
    • 33644999199 scopus 로고    scopus 로고
    • On conditioned reconstruction, gene content data, and the recovery of fusion genomes
    • 10.1016/j.ympev.2005.11.020. 16414287
    • On conditioned reconstruction, gene content data, and the recovery of fusion genomes. CD Bailey MG Fain P Houde, Mol Phylogenet Evol 2006 39 1 263 270 10.1016/j.ympev.2005.11.020 16414287
    • (2006) Mol Phylogenet Evol , vol.39 , Issue.1 , pp. 263-270
    • Bailey, C.D.1    Fain, M.G.2    Houde, P.3
  • 15
    • 57049148533 scopus 로고    scopus 로고
    • The tree of genomes: An empirical comparison of genome-phylogeny reconstruction methods
    • 10.1186/1471-2148-8-312. 19014489
    • The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods. A McCann JA Cotton JO McInerney, BMC Evol Biol 2008 8 312 10.1186/1471-2148-8-312 19014489
    • (2008) BMC Evol Biol , vol.8 , pp. 312
    • McCann, A.1    Cotton, J.A.2    McInerney, J.O.3
  • 16
    • 0348044549 scopus 로고    scopus 로고
    • Genome trees constructed using five different approaches suggest new major bacterial clades
    • 10.1186/1471-2148-1-8. 11734060
    • Genome trees constructed using five different approaches suggest new major bacterial clades. YI Wolf IB Rogozin NV Grishin RL Tatusov EV Koonin, BMC Evol Biol 2001 1 8 10.1186/1471-2148-1-8 11734060
    • (2001) BMC Evol Biol , vol.1 , pp. 8
    • Wolf, Y.I.1    Rogozin, I.B.2    Grishin, N.V.3    Tatusov, R.L.4    Koonin, E.V.5
  • 17
    • 0035843908 scopus 로고    scopus 로고
    • Genes lost and genes found: Evolution of bacterial pathogenesis and symbiosis
    • 10.1126/science.1058543. 11352062
    • Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. H Ochman NA Moran, Science 2001 292 5519 1096 1099 10.1126/science.1058543 11352062
    • (2001) Science , vol.292 , Issue.5519 , pp. 1096-1099
    • Ochman, H.1    Moran, N.A.2
  • 18
    • 33644700003 scopus 로고    scopus 로고
    • Toward automatic reconstruction of a highly resolved tree of life
    • 10.1126/science.1123061. 16513982
    • Toward automatic reconstruction of a highly resolved tree of life. FD Ciccarelli T Doerks C von Mering CJ Creevey B Snel P Bork, Science 2006 311 5765 1283 1287 10.1126/science.1123061 16513982
    • (2006) Science , vol.311 , Issue.5765 , pp. 1283-1287
    • Ciccarelli, F.D.1    Doerks, T.2    Von Mering, C.3    Creevey, C.J.4    Snel, B.5    Bork, P.6
  • 19
    • 19044362395 scopus 로고    scopus 로고
    • Gene family content-based phylogeny of prokaryotes: The effect of criteria for inferring homology
    • 10.1080/10635150590923335. 16012097
    • Gene family content-based phylogeny of prokaryotes: the effect of criteria for inferring homology. AL Hughes V Ekollu R Friedman JR Rose, Syst Biol 2005 54 2 268 276 10.1080/10635150590923335 16012097
    • (2005) Syst Biol , vol.54 , Issue.2 , pp. 268-276
    • Hughes, A.L.1    Ekollu, V.2    Friedman, R.3    Rose, J.R.4
  • 20
    • 0035479142 scopus 로고    scopus 로고
    • Deletional bias and the evolution of bacterial genomes
    • 10.1016/S0168-9525(01)02447-7. 11585665
    • Deletional bias and the evolution of bacterial genomes. A Mira H Ochman NA Moran, Trends Genet 2001 17 10 589 596 10.1016/S0168-9525(01)02447-7 11585665
    • (2001) Trends Genet , vol.17 , Issue.10 , pp. 589-596
    • Mira, A.1    Ochman, H.2    Moran, N.A.3
  • 21
    • 7244221755 scopus 로고    scopus 로고
    • Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous
    • 10.1038/nature02917. 15496922
    • Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. B Kolaczkowski JW Thornton, Nature 2004 431 7011 980 984 10.1038/nature02917 15496922
    • (2004) Nature , vol.431 , Issue.7011 , pp. 980-984
    • Kolaczkowski, B.1    Thornton, J.W.2
  • 22
    • 17744400517 scopus 로고    scopus 로고
    • Likelihood, parsimony, and heterogeneous evolution
    • 10.1093/molbev/msi123. 15746012
    • Likelihood, parsimony, and heterogeneous evolution. M Spencer E Susko AJ Roger, Mol Biol Evol 2005 22 5 1161 1164 10.1093/molbev/msi123 15746012
    • (2005) Mol Biol Evol , vol.22 , Issue.5 , pp. 1161-1164
    • Spencer, M.1    Susko, E.2    Roger, A.J.3
  • 23
    • 67749145407 scopus 로고    scopus 로고
    • A phylogenetic mixture model for gene family loss in parasitic bacteria
    • 19435739
    • A phylogenetic mixture model for gene family loss in parasitic bacteria. M Spencer A Sangaralingam, Mol Biol Evol 2009 19435739
    • (2009) Mol Biol Evol
    • Spencer, M.1    Sangaralingam, A.2
  • 24
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • 10.1126/science.278.5338.631. 9381173
    • A genomic perspective on protein families. RL Tatusov EV Koonin DJ Lipman, Science 1997 278 5338 631 637 10.1126/science.278.5338.631 9381173
    • (1997) Science , vol.278 , Issue.5338 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 25
    • 0043163718 scopus 로고    scopus 로고
    • Protein families and TRIBES in genome sequence space
    • 10.1093/nar/gkg495. 12888524
    • Protein families and TRIBES in genome sequence space. AJ Enright V Kunin CA Ouzounis, Nucleic Acids Res 2003 31 15 4632 4638 10.1093/nar/gkg495 12888524
    • (2003) Nucleic Acids Res , vol.31 , Issue.15 , pp. 4632-4638
    • Enright, A.J.1    Kunin, V.2    Ouzounis, C.A.3
  • 27
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • 10.1093/nar/30.7.1575. 11917018
    • An efficient algorithm for large-scale detection of protein families. AJ Enright S Van Dongen CA Ouzounis, Nucleic Acids research 2002 30 7 10.1093/nar/30.7.1575 11917018
    • (2002) Nucleic Acids Research , vol.30 , Issue.7
    • Enright, A.J.1    Van Dongen, S.2    Ouzounis, C.A.3
  • 29
    • 0030807655 scopus 로고    scopus 로고
    • BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data
    • 9254330
    • BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. O Gascuel, Mol Biol Evol 1997 14 7 685 695 9254330
    • (1997) Mol Biol Evol , vol.14 , Issue.7 , pp. 685-695
    • Gascuel, O.1
  • 33
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • 10.1080/10635150390235520. 14530136
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. S Guindon O Gascuel, Syst Biol 2003 52 5 696 704 10.1080/10635150390235520 14530136
    • (2003) Syst Biol , vol.52 , Issue.5 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 34
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • DOI 10.1016/0025-5564(81)90043-2
    • Comparison of phylogenetic trees. DR Robinson LR Foulds, Mathematical Biosciences 1981 53 131 147 10.1016/0025-5564(81)90043-2 (Pubitemid 11129084)
    • (1981) Mathematical Biosciences , vol.53 , Issue.1-2 , pp. 131-147
    • Robinson, D.F.1    Foulds, L.R.2
  • 35
    • 9744258014 scopus 로고    scopus 로고
    • Genome reduction in prokaryotic obligatory intracellular parasites of humans: A comparative analysis
    • 10.1099/ijs.0.63090-0. 15545414
    • Genome reduction in prokaryotic obligatory intracellular parasites of humans: a comparative analysis. KR Sakharkar PK Dhar VT Chow, Int J Syst Evol Microbiol 2004 54 Pt 6 1937 1941 10.1099/ijs.0.63090-0 15545414
    • (2004) Int J Syst Evol Microbiol , vol.54 , Issue.PART 6 , pp. 1937-1941
    • Sakharkar, K.R.1    Dhar, P.K.2    Chow, V.T.3
  • 36
    • 3042840997 scopus 로고    scopus 로고
    • Computational inference of scenarios for alpha-proteobacterial genome evolution
    • 10.1073/pnas.0400975101. 15210995
    • Computational inference of scenarios for alpha-proteobacterial genome evolution. B Boussau EO Karlberg AC Frank BA Legault SG Andersson, Proc Natl Acad Sci USA 2004 101 26 9722 9727 10.1073/pnas.0400975101 15210995
    • (2004) Proc Natl Acad Sci USA , vol.101 , Issue.26 , pp. 9722-9727
    • Boussau, B.1    Karlberg, E.O.2    Frank, A.C.3    Legault, B.A.4    Andersson, S.G.5
  • 37
    • 0036078078 scopus 로고    scopus 로고
    • Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
    • 12045149
    • Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. IK Jordan IB Rogozin YI Wolf EV Koonin, Genome Res 2002 12 6 962 968 12045149
    • (2002) Genome Res , vol.12 , Issue.6 , pp. 962-968
    • Jordan, I.K.1    Rogozin, I.B.2    Wolf, Y.I.3    Koonin, E.V.4
  • 38
    • 0036898759 scopus 로고    scopus 로고
    • Prokaryotic evolution in light of gene transfer
    • 12446813
    • Prokaryotic evolution in light of gene transfer. JP Gogarten WF Doolittle JG Lawrence, Mol Biol Evol 2002 19 12 2226 2238 12446813
    • (2002) Mol Biol Evol , vol.19 , Issue.12 , pp. 2226-2238
    • Gogarten, J.P.1    Doolittle, W.F.2    Lawrence, J.G.3
  • 39
    • 30344486571 scopus 로고    scopus 로고
    • On the desirability of models for inferring genome phylogenies
    • 10.1016/j.tim.2005.10.006. 16271477
    • On the desirability of models for inferring genome phylogenies. JO McInerney, Trends Microbiol 2006 14 1 1 2 10.1016/j.tim.2005.10.006 16271477
    • (2006) Trends Microbiol , vol.14 , Issue.1 , pp. 1-2
    • McInerney, J.O.1
  • 41
    • 45249114886 scopus 로고    scopus 로고
    • Uncovering rate variation of lateral gene transfer during bacterial genome evolution
    • 18492275
    • Uncovering rate variation of lateral gene transfer during bacterial genome evolution. W Hao BG Golding, BMC Genomics 2008 9 235 18492275
    • (2008) BMC Genomics , vol.9 , Issue.235
    • Hao, W.1    Golding, B.G.2
  • 42
    • 38649092410 scopus 로고    scopus 로고
    • Dendroscope: An interactive viewer for large phylogenetic trees
    • 10.1186/1471-2105-8-460. 18034891
    • Dendroscope: An interactive viewer for large phylogenetic trees. DH Huson DC Richter C Rausch T Dezulian M Franz R Rupp, BMC Bioinformatics 2007 8 460 10.1186/1471-2105-8-460 18034891
    • (2007) BMC Bioinformatics , vol.8 , pp. 460
    • Huson, D.H.1    Richter, D.C.2    Rausch, C.3    Dezulian, T.4    Franz, M.5    Rupp, R.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.