메뉴 건너뛰기




Volumn 29, Issue 6, 2012, Pages 1557-1568

Collodictyon-an ancient lineage in the tree of eukaryotes

Author keywords

18S and 28S rDNA; CDNA, pyrosequencing; Collodictyon; Diphyllatia; Phylogenomics; Tree of life

Indexed keywords

COMPLEMENTARY DNA; DNA 18S; RIBOSOME DNA;

EID: 84861386206     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mss001     Document Type: Article
Times cited : (74)

References (54)
  • 2
    • 0033015732 scopus 로고    scopus 로고
    • Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies
    • Brinkmann H, Philippe H. 1999. Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies. Mol Biol Evol. 16:817-825. (Pubitemid 29260835)
    • (1999) Molecular Biology and Evolution , vol.16 , Issue.6 , pp. 817-825
    • Brinkmann, H.1    Philippe, H.2
  • 3
    • 0036010839 scopus 로고    scopus 로고
    • Collodictyon triciliatum and Diphylleia rotans (= Aulacomonas submarina) form a new family of flagellates (Collodictyonidae) with tubular mitochondrial cristae that is phylogenetically distant from other flagellate groups
    • Brugerolle G, Bricheux G, Philippe H, Coffe G. 2002. Collodictyon triciliatum and Diphylleia rotans (5Aulacomonas submarina) form a new family of flagellates (Collodictyonidae) with tubular mitochondrial cristae that is phylogenetically distant from other flagellate groups. Protist 153:59-70. (Pubitemid 34414183)
    • (2002) Protist , vol.153 , Issue.1 , pp. 59-70
    • Brugerolle, G.U.Y.1    Bricheux, G.2    Philippe, H.3    Coffe, G.4
  • 4
    • 73149097943 scopus 로고    scopus 로고
    • Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, Telonemia and Centroheliozoa, are related to photosynthetic chromalveolates
    • (14 co-authors)
    • Burki F, Inagaki Y, Bra°te J, et al. (14 co-authors). 2009. Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, Telonemia and Centroheliozoa, are related to photosynthetic chromalveolates. Genome Biol Evol. 1:231-238.
    • (2009) Genome Biol Evol. , vol.1 , pp. 231-238
    • Burki, F.1    Inagaki, Y.2    Brate, J.3
  • 7
    • 46949092431 scopus 로고    scopus 로고
    • Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes
    • DOI 10.1098/rsbl.2008.0224, PII J355M22278421402
    • Burki F, Shalchian-Tabrizi K, Pawlowski J. 2008. Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes. Biol Lett. 4:366-369. (Pubitemid 351961461)
    • (2008) Biology Letters , vol.4 , Issue.4 , pp. 366-369
    • Burki, F.1    Shalchian-Tabrizi, K.2    Pawlowski, J.3
  • 8
    • 0001991291 scopus 로고
    • On the fresh-and salt-water Rhizopoda of England and India
    • Carter HJ. 1865. On the fresh-and salt-water Rhizopoda of England and India. Ann Mag Nat Hist. 15:227-293.
    • (1865) Ann Mag Nat Hist. , vol.15 , pp. 227-293
    • Carter, H.J.1
  • 9
    • 0034043778 scopus 로고    scopus 로고
    • Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    • Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 17:540-552. (Pubitemid 30210700)
    • (2000) Molecular Biology and Evolution , vol.17 , Issue.4 , pp. 540-552
    • Castresana, J.1
  • 10
    • 0027145102 scopus 로고
    • Kingdom protozoa and its 18 phyla
    • Cavalier-Smith T. 1993. Kingdom protozoa and its 18 phyla. Microbiol Rev. 57:953-994. (Pubitemid 24004511)
    • (1993) Microbiological Reviews , vol.57 , Issue.4 , pp. 953-994
    • Cavalier-Smith, T.1
  • 11
    • 0003265745 scopus 로고    scopus 로고
    • The excavate protozoan phyla Metamonada Grassé emend. (Anaeromonadea, Parabasalia, Carpediemonas, Eopharyngia) and Loukozoa emend. (Jakobea, Malawimonas): Their evolutionary affinities and new higher taxa
    • DOI 10.1099/ijs.0.02548-0
    • Cavalier-Smith T. 2003. The excavate protozoan phyla Metamonada Grasse emend. (Anaeromonadea, Parabasalia, Carpediemonas, Eopharyngia) and Loukozoa emend. (Jakobea, Malawimonas): their evolutionary affinities and new higher taxa. Int J Syst Evol Microbiol. 53:1741-1758. (Pubitemid 37483830)
    • (2003) International Journal of Systematic and Evolutionary Microbiology , vol.53 , Issue.6 , pp. 1741-1758
    • Cavalier-Smith, T.1
  • 12
    • 77954090275 scopus 로고    scopus 로고
    • Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree
    • Cavalier-Smith T. 2010. Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree. Biol Lett. 6:342-345.
    • (2010) Biol Lett. , vol.6 , pp. 342-345
    • Cavalier-Smith, T.1
  • 13
    • 79954529507 scopus 로고    scopus 로고
    • ProtTest 3: Fast selection of best-fit models of protein evolution
    • Darriba D, Taboada GL, Doallo R, Posada D. 2011. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27:1164-1165.
    • (2011) Bioinformatics , vol.27 , pp. 1164-1165
    • Darriba, D.1    Taboada, G.L.2    Doallo, R.3    Posada, D.4
  • 14
    • 84858411861 scopus 로고    scopus 로고
    • Rooting the eukaryotic tree with mitochondrial and bacterial proteins
    • Advance Access published December 1, 2011 doi:10.1093/molbev/msr295
    • Derelle R, Lang BF. 2011. Rooting the eukaryotic tree with mitochondrial and bacterial proteins. Mol Biol Evol. Advance Access published December 1, 2011. doi:10.1093/molbev/msr295.
    • (2011) Mol Biol Evol.
    • Derelle, R.1    Lang, B.F.2
  • 15
    • 47949090280 scopus 로고    scopus 로고
    • PHYLIP (phylogeny inference package)
    • Seattle (WA): Department of Genetics, University of Washington
    • Felsenstein J. 2001. PHYLIP (phylogeny inference package). 3.6. Distributed by the author. Seattle (WA): Department of Genetics, University of Washington.
    • (2001) 3.6. Distributed by the Author
    • Felsenstein, J.1
  • 16
    • 0021016329 scopus 로고
    • A simple and very efficient method for generating cDNA libraries
    • Gubler U, Hoffman BJ. 1983. A simple and very efficient method for generating cDNA libraries. Gene 25:263-269. (Pubitemid 14204652)
    • (1983) Gene , vol.25 , Issue.2-3 , pp. 263-269
    • Gubler, U.1    Hoffman, B.J.2
  • 17
    • 84988179817 scopus 로고
    • Yellow-green algae with chlorophyllide c
    • Guillard RRL, Lorenzen CJ. 1972. Yellow-green algae with chlorophyllide c. J Phycol. 8:10-14.
    • (1972) J Phycol. , vol.8 , pp. 10-14
    • Guillard, R.R.L.1    Lorenzen, C.J.2
  • 18
  • 19
    • 10344254308 scopus 로고    scopus 로고
    • Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I
    • DOI 10.1038/nature03149
    • Hrdy I, Hirt RP, Dolezal P, Bardonova L, Foster PG, Tachezy J, Embley TM. 2004. Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I. Nature 432:618-622. (Pubitemid 39626267)
    • (2004) Nature , vol.432 , Issue.7017 , pp. 618-622
    • Hrdy, I.1    Hirt, R.P.2    Dolezal, P.3    Bardonova, L.4    Foster, P.G.5    Tachezy, J.6    Embley, T.M.7
  • 20
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES: Bayesian inference of phylogenetic trees
    • Huelsenbeck JP, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755. (Pubitemid 32851390)
    • (2001) Bioinformatics , vol.17 , Issue.8 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 21
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30:3059-3066. (Pubitemid 34851225)
    • (2002) Nucleic Acids Research , vol.30 , Issue.14 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.-I.3    Miyata, T.4
  • 23
    • 33750957132 scopus 로고    scopus 로고
    • Evolutionary relationships of apusomonads inferred from taxon-rich analyses of 6 nuclear encoded genes
    • DOI 10.1093/molbev/msl120
    • Kim E, Simpson AG, Graham LE. 2006. Evolutionary relationships of apusomonads inferred from taxon-rich analyses of 6 nuclear encoded genes. Mol Biol Evol. 23:2455-2466. (Pubitemid 44737139)
    • (2006) Molecular Biology and Evolution , vol.23 , Issue.12 , pp. 2455-2466
    • Kim, E.1    Simpson, A.G.B.2    Graham, L.E.3
  • 24
    • 0002630463 scopus 로고
    • Collodictyon triciliatum H.J. Carter (1865)-a common but fixation-sensitive algivorous flagellate from the limnopelagial
    • Klaveness D. 1995. Collodictyon triciliatum H.J. Carter (1865)-a common but fixation-sensitive algivorous flagellate from the limnopelagial. Nord J Freshw Res. 70:3-11.
    • (1995) Nord J Freshw Res. , vol.70 , pp. 3-11
    • Klaveness, D.1
  • 26
    • 2442691520 scopus 로고    scopus 로고
    • A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
    • DOI 10.1093/molbev/msh112
    • Lartillot N, Philippe H. 2004. A Bayesian mixture model for acrosssite heterogeneities in the amino-acid replacement process. Mol Biol Evol. 21:1095-1109. (Pubitemid 38658218)
    • (2004) Molecular Biology and Evolution , vol.21 , Issue.6 , pp. 1095-1109
    • Lartillot, N.1    Philippe, H.2
  • 29
    • 70349382868 scopus 로고    scopus 로고
    • Molecular phylogeny and description of the novel katablepharid Roombia truncata gen et sp. nov., and establishment of the Hacrobia taxon nov
    • Okamoto N, Chantangsi C, Horak A, Leander BS, Keeling PJ. 2009. Molecular phylogeny and description of the novel katablepharid Roombia truncata gen. et sp. nov., and establishment of the Hacrobia taxon nov. PLoS One 4:e7080.
    • (2009) PLoS One , vol.4
    • Okamoto, N.1    Chantangsi, C.2    Horak, A.3    Leander, B.S.4    Keeling, P.J.5
  • 32
    • 34247899047 scopus 로고    scopus 로고
    • Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages
    • DOI 10.1016/j.cub.2007.03.069, PII S0960982207012559
    • Patron NJ, Inagaki Y, Keeling PJ. 2007. Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages. Curr Biol. 17:887-891. (Pubitemid 46702668)
    • (2007) Current Biology , vol.17 , Issue.10 , pp. 887-891
    • Patron, N.J.1    Inagaki, Y.2    Keeling, P.J.3
  • 33
    • 0032744297 scopus 로고    scopus 로고
    • The diversity of eukaryotes
    • Patterson DJ. 1999. The diversity of eukaryotes. Am Nat. 154: S96-S124.
    • (1999) Am Nat. , vol.154
    • Patterson, D.J.1
  • 34
    • 85050111332 scopus 로고
    • Binary fission in Collodictyon triciliatum carter
    • Berkeley (CA): University of California
    • Rhodes RC. 1917. Binary fission in Collodictyon triciliatum carter. The faculty of the college of letters and science. Berkeley (CA): University of California. p. 74.
    • (1917) The Faculty of the College of Letters and Science , pp. 74
    • Rhodes, R.C.1
  • 35
    • 24144503755 scopus 로고    scopus 로고
    • Myosin domain evolution and the primary divergence of eukaryotes
    • DOI 10.1038/nature03949
    • Richards TA, Cavalier-Smith T. 2005. Myosin domain evolution and the primary divergence of eukaryotes. Nature 436: 1113-1118. (Pubitemid 41232283)
    • (2005) Nature , vol.436 , Issue.7054 , pp. 1113-1118
    • Richards, T.A.1    Cavalier-Smith, T.2
  • 36
    • 34547883900 scopus 로고    scopus 로고
    • Toward resolving the eukaryotic tree: The phylogenetic positions of jakobids and cercozoans
    • DOI 10.1016/j.cub.2007.07.036, PII S0960982207017162
    • Rodriguez-Ezpeleta N, Brinkmann H, Burger G, Roger AJ, Gray MW, Philippe H, Lang BF. 2007. Toward resolving the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans. Curr Biol. 17:1420-1425. (Pubitemid 47259385)
    • (2007) Current Biology , vol.17 , Issue.16 , pp. 1420-1425
    • Rodriguez-Ezpeleta, N.1    Brinkmann, H.2    Burger, G.3    Roger, A.J.4    Gray, M.W.5    Philippe, H.6    Lang, B.F.7
  • 37
    • 60349108359 scopus 로고    scopus 로고
    • Evolution: Revisiting the root of the eukaryote tree
    • Roger AJ, Simpson AG. 2009. Evolution: revisiting the root of the eukaryote tree. Curr Biol. 19:R165-R167.
    • (2009) Curr Biol. , vol.19
    • Roger, A.J.1    Simpson, A.G.2
  • 38
    • 77953231719 scopus 로고    scopus 로고
    • Analysis of rare genomic changes does not support the unikont-bikont phylogeny and suggests cyanobacterial symbiosis as the point of primary radiation of eukaryotes
    • Rogozin IB, Basu MK, Csuros M, Koonin EV. 2009. Analysis of rare genomic changes does not support the unikont-bikont phylogeny and suggests cyanobacterial symbiosis as the point of primary radiation of eukaryotes. Genome Biol Evol. 1:99-113.
    • (2009) Genome Biol Evol. , vol.1 , pp. 99-113
    • Rogozin, I.B.1    Basu, M.K.2    Csuros, M.3    Koonin, E.V.4
  • 39
    • 34248188251 scopus 로고    scopus 로고
    • SCaFoS: A tool for selection, concatenation and fusion of sequences for phylogenomics
    • Roure B, Rodriguez-Ezpeleta N, Philippe H. 2007. SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics. BMC Evol Biol. 7(Suppl 1):S2.
    • (2007) BMC Evol Biol. , vol.7 , Issue.SUPPL. 1
    • Roure, B.1    Rodriguez-Ezpeleta, N.2    Philippe, H.3
  • 40
    • 51649088380 scopus 로고    scopus 로고
    • Diversification of unicellular eukaryotes: Cryptomonad colonizations of marine and fresh waters inferred from revised 18S rRNA phylogeny
    • Shalchian-Tabrizi K, Bra°te J, Logares R, Klaveness D, Berney C, Jakobsen KS. 2008. Diversification of unicellular eukaryotes: cryptomonad colonizations of marine and fresh waters inferred from revised 18S rRNA phylogeny. Environ Microbiol. 10:2635-2644.
    • (2008) Environ Microbiol. , vol.10 , pp. 2635-2644
    • Shalchian-Tabrizi, K.1    Brate, J.2    Logares, R.3    Klaveness, D.4    Berney, C.5    Jakobsen, K.S.6
  • 43
    • 0036623258 scopus 로고    scopus 로고
    • An approximately unbiased test of phylogenetic tree selection
    • DOI 10.1080/10635150290069913
    • Shimodaira H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst Biol. 51:492-508. (Pubitemid 35180700)
    • (2002) Systematic Biology , vol.51 , Issue.3 , pp. 492-508
    • Shimodaira, H.1
  • 44
    • 0036139287 scopus 로고    scopus 로고
    • CONSEL: For assessing the confidence of phylogenetic tree selection
    • Shimodaira H, Hasegawa M. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246-1247. (Pubitemid 33735360)
    • (2001) Bioinformatics , vol.17 , Issue.12 , pp. 1246-1247
    • Shimodaira, H.1    Hasegawa, M.2
  • 45
    • 0345328163 scopus 로고    scopus 로고
    • Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota)
    • DOI 10.1099/ijs.0.02578-0
    • Simpson AGB. 2003. Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota). Int J Syst Evol Microbiol. 53:1759-1777. (Pubitemid 37483831)
    • (2003) International Journal of Systematic and Evolutionary Microbiology , vol.53 , Issue.6 , pp. 1759-1777
    • Simpson, A.G.B.1
  • 46
    • 12544255323 scopus 로고    scopus 로고
    • The real 'kingdoms' of eukaryotes
    • Simpson AGB, Roger AJ. 2004. The real 'kingdoms' of eukaryotes. Curr Biol. 14:R693-R696.
    • (2004) Curr Biol. , vol.14
    • Simpson, A.G.B.1    Roger, A.J.2
  • 47
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • DOI 10.1093/bioinformatics/btl446
    • Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690. (Pubitemid 44642609)
    • (2006) Bioinformatics , vol.22 , Issue.21 , pp. 2688-2690
    • Stamatakis, A.1
  • 48
    • 50249100595 scopus 로고    scopus 로고
    • A rapid bootstrap algorithm for the RAxML Web servers
    • Stamatakis A, Hoover P, Rougemont J. 2008. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol. 57:758-771.
    • (2008) Syst Biol. , vol.57 , pp. 758-771
    • Stamatakis, A.1    Hoover, P.2    Rougemont, J.3
  • 49
    • 0037025197 scopus 로고    scopus 로고
    • Rooting the eukaryote tree by using a derived gene fusion
    • DOI 10.1126/science.1071196
    • Stechmann A, Cavalier-Smith T. 2002. Rooting the eukaryote tree by using a derived gene fusion. Science 297:89-91. (Pubitemid 34743097)
    • (2002) Science , vol.297 , Issue.5578 , pp. 89-91
    • Stechmann, A.1    Cavalier-Smith, T.2
  • 50
    • 70350502569 scopus 로고    scopus 로고
    • PROCOV: Maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis
    • Wang HC, Susko E, Roger AJ. 2009. PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis. BMC Evol Biol. 9:225.
    • (2009) BMC Evol Biol. , vol.9 , pp. 225
    • Wang, H.C.1    Susko, E.2    Roger, A.J.3
  • 51
    • 77955656595 scopus 로고    scopus 로고
    • Palpitomonas bilix gen. et sp. nov.: A novel deep-branching heterotroph possibly related to Archaeplastida or Hacrobia
    • Yabuki A, Inagaki Y, Ishida K. 2010. Palpitomonas bilix gen. et sp. nov.: a novel deep-branching heterotroph possibly related to Archaeplastida or Hacrobia. Protist 161:523-538.
    • (2010) Protist , vol.161 , pp. 523-538
    • Yabuki, A.1    Inagaki, Y.2    Ishida, K.3
  • 52
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • DOI 10.1093/molbev/msm088
    • Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591. (Pubitemid 47236688)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.8 , pp. 1586-1591
    • Yang, Z.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.