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Volumn 6, Issue 3, 2014, Pages 474-481

Archaeal "dark matter" and the origin of eukaryotes

Author keywords

"Dark matter"; Eukaryogenesis; Phylogenetics; Tree of Life

Indexed keywords

" DARK MATTER"; ARCHAEAL GENOME; ARCHAEON; ARTICLE; BIOLOGICAL MODEL; EUKARYOGENESIS; EUKARYOTE; EVOLUTION; GENETICS; MITOCHONDRION; PHYLOGENY; SEQUENCE ALIGNMENT; TREE OF LIFE;

EID: 84901195821     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evu031     Document Type: Article
Times cited : (78)

References (50)
  • 1
    • 33845898858 scopus 로고    scopus 로고
    • Lineages of acidophilic archaea revealed by community genomic analysis
    • Baker BJ, et al. 2006. Lineages of acidophilic archaea revealed by community genomic analysis. Science 314: 1933-1935.
    • (2006) Science , vol.314 , pp. 1933-1935
    • Baker, B.J.1
  • 2
    • 0035986890 scopus 로고    scopus 로고
    • Bayesian model adequacy and choice in phylogenetics
    • Bollback JP. 2002. Bayesian model adequacy and choice in phylogenetics. Mol Biol Evol. 19: 1171-1180.
    • (2002) Mol Biol Evol , vol.19 , pp. 1171-1180
    • Bollback, J.P.1
  • 3
    • 67049158348 scopus 로고    scopus 로고
    • Fast statistical alignment
    • Bradley RK, et al. 2009. Fast statistical alignment. PLoS Comput Biol. 5: e1000392.
    • (2009) PLoS Comput Biol , vol.5
    • Bradley, R.K.1
  • 4
    • 39149118031 scopus 로고    scopus 로고
    • Mesophilic Crenarchaeota: Proposal for a third archaeal phylum, the Thaumarchaeota
    • Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P. 2008. Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol. 6: 245-252.
    • (2008) Nat Rev Microbiol , vol.6 , pp. 245-252
    • Brochier-Armanet, C.1    Boussau, B.2    Gribaldo, S.3    Forterre, P.4
  • 5
    • 79959307333 scopus 로고    scopus 로고
    • Phylogeny and evolution of the Archaea: One hundred genomes later
    • Brochier-Armanet C, Forterre P, Gribaldo S. 2011. Phylogeny and evolution of the Archaea: one hundred genomes later. Curr Opin Microbiol. 14: 274-281.
    • (2011) Curr Opin Microbiol , vol.14 , pp. 274-281
    • Brochier-Armanet, C.1    Forterre, P.2    Gribaldo, S.3
  • 6
    • 33846349924 scopus 로고    scopus 로고
    • Rooting the tree of life by transition analyses
    • Cavalier-Smith T. 2006. Rooting the tree of life by transition analyses. Biol Direct. 1: 19.
    • (2006) Biol Direct , vol.1 , pp. 19
    • Cavalier-Smith, T.1
  • 8
    • 77954403053 scopus 로고    scopus 로고
    • BMGE (Block Mapping and Gathering with Entropy): A new software for selection of phylogenetic informative regions from multiple sequence alignments
    • Criscuolo A, Gribaldo S. 2010. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol. 10: 210.
    • (2010) BMC Evol Biol , vol.10 , pp. 210
    • Criscuolo, A.1    Gribaldo, S.2
  • 9
    • 77958506738 scopus 로고    scopus 로고
    • Genome networks root the tree of life between prokaryotic domains
    • Dagan T, Roettger M, Bryant D, Martin W. 2010. Genome networks root the tree of life between prokaryotic domains. Genome Biol Evol. 2: 379-392.
    • (2010) Genome Biol Evol , vol.2 , pp. 379-392
    • Dagan, T.1    Roettger, M.2    Bryant, D.3    Martin, W.4
  • 10
    • 84895751645 scopus 로고    scopus 로고
    • PhyloSift: Phylogenetic analysis of genomes and metagenomes
    • Darling A, et al. 2014. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ. 2:e243.
    • (2014) PeerJ , vol.2
    • Darling, A.1
  • 11
    • 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
  • 12
    • 33845627286 scopus 로고    scopus 로고
    • The supermatrix approach to systematics
    • de Queiroz A, Gatesy J. 2007. The supermatrix approach to systematics. Trends Ecol Evol. 22: 34-41.
    • (2007) Trends Ecol Evol , vol.22 , pp. 34-41
    • De Queiroz, A.1    Gatesy, J.2
  • 13
    • 14644430471 scopus 로고    scopus 로고
    • ProbCons: Probabilistic consistency-basedmultiple sequence alignment
    • Do CB, Mahabhashyam MS, Brudno M, Batzoglou S. 2005. ProbCons: probabilistic consistency-basedmultiple sequence alignment. Genome Res. 15: 330-340.
    • (2005) Genome Res , vol.15 , pp. 330-340
    • Do, C.B.1    Mahabhashyam, M.S.2    Brudno, M.3    Batzoglou, S.4
  • 14
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 15
    • 45849112155 scopus 로고    scopus 로고
    • A korarchaeal genome reveals insights into the evolution of the Archaea
    • Elkins JG, et al. 2008. A korarchaeal genome reveals insights into the evolution of the Archaea. Proc Natl Acad Sci U S A. 105: 8102-8107.
    • (2008) Proc Natl Acad Sci U S A. , vol.105 , pp. 8102-8107
    • Elkins, J.G.1
  • 16
    • 67651039738 scopus 로고    scopus 로고
    • The primary divisions of life: A phylogenomic approach employing composition-heterogeneous methods
    • Foster PG, Cox CJ, Embley TM. 2009. The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods. Phil Trans R Soc B. 364: 2197-2207.
    • (2009) Phil Trans R Soc B. , vol.364 , pp. 2197-2207
    • Foster, P.G.1    Cox, C.J.2    Embley, T.M.3
  • 17
    • 0024722874 scopus 로고
    • Evolution of the vacuolar H+-ATPase: Implications for the origin of eukaryotes
    • Gogarten JP, et al. 1989. Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes. Proc Natl Acad Sci U S A. 86: 6661-6665.
    • (1989) Proc Natl Acad Sci U S A. , vol.86 , pp. 6661-6665
    • Gogarten, J.P.1
  • 18
    • 0032025857 scopus 로고    scopus 로고
    • Is it better to add taxa or characters to a difficult phylogenetic problem?
    • Graybeal A. 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst Biol. 47: 9-17.
    • (1998) Syst Biol , vol.47 , pp. 9-17
    • Graybeal, A.1
  • 19
    • 82355180998 scopus 로고    scopus 로고
    • The Archaeal 'TACK' superphylum and the origin of eukaryotes
    • Guy L, Ettema TJ. 2011. The archaeal 'TACK' superphylum and the origin of eukaryotes. Trends Microbiol. 19: 580-587.
    • (2011) Trends Microbiol , vol.19 , pp. 580-587
    • Guy, L.1    Ettema, T.J.2
  • 20
    • 0024358140 scopus 로고
    • Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes
    • Iwabe N, Kuma K, Hasegawa M, Osawa S, Miyata T. 1989. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc Natl Acad Sci U S A. 86: 9355-9359.
    • (1989) Proc Natl Acad Sci U S A. , vol.86 , pp. 9355-9359
    • Iwabe, N.1    Kuma, K.2    Hasegawa, M.3    Osawa, S.4    Miyata, T.5
  • 21
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 8: 275-282.
    • (1992) Comput Appl Biosci , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 22
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: Improvement in accuracy of multiple sequence alignment
    • Katoh K, Kuma K, Toh H, Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33: 511-518.
    • (2005) Nucleic Acids Res , vol.33 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4
  • 23
    • 0031038402 scopus 로고    scopus 로고
    • Evidence that eukaryotic triosephosphate isomerase is of alpha-proteobacterial origin
    • Keeling PJ, Doolittle WF. 1997. Evidence that eukaryotic triosephosphate isomerase is of alpha-proteobacterial origin. Proc Natl Acad Sci U S A. 94: 1270-1275.
    • (1997) Proc Natl Acad Sci U S A. , vol.94 , pp. 1270-1275
    • Keeling, P.J.1    Doolittle, W.F.2
  • 24
    • 84874964884 scopus 로고    scopus 로고
    • Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes
    • Kelly S, Wickstead B, Gull K. 2011. Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes. Proc Biol Sci. 278: 1009-1018.
    • (2011) Proc Biol Sci , vol.278 , pp. 1009-1018
    • Kelly, S.1    Wickstead, B.2    Gull, K.3
  • 25
    • 0039861672 scopus 로고
    • Eocytes: A new ribosome structure indicates a kingdom with a close relationship to eukaryotes
    • Lake JA, Henderson E, Oakes M, Clark MW. 1984. Eocytes: a new ribosome structure indicates a kingdom with a close relationship to eukaryotes. Proc Natl Acad Sci U S A. 81: 3786-3790.
    • (1984) Proc Natl Acad Sci U S A. , vol.81 , pp. 3786-3790
    • Lake, J.A.1    Henderson, E.2    Oakes, M.3    Clark, M.W.4
  • 27
    • 34248159030 scopus 로고    scopus 로고
    • Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model
    • Lartillot N, Brinkmann H, Philippe H. 2007. Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol Biol. 7(Suppl 1):S4.
    • (2007) BMC Evol Biol , vol.7 , Issue.SUPPL. 1
    • Lartillot, N.1    Brinkmann, H.2    Philippe, H.3
  • 28
    • 69949126557 scopus 로고    scopus 로고
    • PhyloBayes 3: A Bayesian software package for phylogenetic reconstruction and molecular dating
    • Lartillot N, Lepage T, Blanquart S. 2009. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25: 2286-2288.
    • (2009) Bioinformatics , vol.25 , pp. 2286-2288
    • Lartillot, N.1    Lepage, T.2    Blanquart, S.3
  • 29
    • 2442691520 scopus 로고    scopus 로고
    • A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
    • Lartillot N, Philippe H. 2004. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol. 21: 1095-1109.
    • (2004) Mol Biol Evol , vol.21 , pp. 1095-1109
    • Lartillot, N.1    Philippe, H.2
  • 30
    • 84881629698 scopus 로고    scopus 로고
    • PhyloBayes MPI: Phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment
    • Lartillot N, Rodrigue N, Stubbs D, Richer J. 2013. PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst Biol. 62: 611-615.
    • (2013) Syst Biol , vol.62 , pp. 611-615
    • Lartillot, N.1    Rodrigue, N.2    Stubbs, D.3    Richer, J.4
  • 31
    • 84880261576 scopus 로고    scopus 로고
    • The effects of model choice and mitigating bias on the ribosomal tree of life
    • Lasek-Nesselquist E, Gogarten JP. 2013. The effects of model choice and mitigating bias on the ribosomal tree of life. Mol Phylogenet Evol. 69: 17-38.
    • (2013) Mol Phylogenet Evol , vol.69 , pp. 17-38
    • Lasek-Nesselquist, E.1    Gogarten, J.P.2
  • 32
    • 29244447181 scopus 로고    scopus 로고
    • Kalign - An accurate and fast multiple sequence alignment algorithm
    • Lassmann T, Sonnhammer EL. 2005. Kalign - an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics 6: 298.
    • (2005) BMC Bioinformatics , vol.6 , pp. 298
    • Lassmann, T.1    Sonnhammer, E.L.2
  • 33
    • 45849154166 scopus 로고    scopus 로고
    • An improved general amino acid replacement matrix
    • Le SQ, Gascuel O. 2008. An improved general amino acid replacement matrix. Mol Biol Evol. 25: 1307-1320.
    • (2008) Mol Biol Evol , vol.25 , pp. 1307-1320
    • Le, S.Q.1    Gascuel, O.2
  • 34
    • 34547540925 scopus 로고    scopus 로고
    • Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth
    • Marcy Y, et al. 2007. Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci U S A. 104: 11889-11894.
    • (2007) Proc Natl Acad Sci U S A. , vol.104 , pp. 11889-11894
    • Marcy, Y.1
  • 35
    • 2642689666 scopus 로고    scopus 로고
    • The hydrogen hypothesis for the first eukaryote
    • Martin W, Muller M. 1998. The hydrogen hypothesis for the first eukaryote. Nature 392: 37-41.
    • (1998) Nature , vol.392 , pp. 37-41
    • Martin, W.1    Muller, M.2
  • 36
    • 84355162254 scopus 로고    scopus 로고
    • De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities
    • Narasingarao P, et al. 2012. De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J. 6: 81-93.
    • (2012) ISME J. , vol.6 , pp. 81-93
    • Narasingarao, P.1
  • 37
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame C, Higgins DG, Heringa J. 2000. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol. 302: 205-217.
    • (2000) J Mol Biol , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 38
    • 79955598535 scopus 로고    scopus 로고
    • Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group
    • Nunoura T, et al. 2011. Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res. 39: 3204-3223.
    • (2011) Nucleic Acids Res , vol.39 , pp. 3204-3223
    • Nunoura, T.1
  • 39
    • 79959289950 scopus 로고    scopus 로고
    • The Thaumarchaeota: An emerging view of their phylogeny and ecophysiology
    • Pester M, Schleper C, Wagner M. 2011. The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology. Curr Opin Microbiol. 14: 300-306.
    • (2011) Curr Opin Microbiol , vol.14 , pp. 300-306
    • Pester, M.1    Schleper, C.2    Wagner, M.3
  • 40
    • 79953716259 scopus 로고    scopus 로고
    • Resolving difficult phylogenetic questions: Why more sequences are not enough
    • Philippe H, et al. 2011. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol. 9:e1000602.
    • (2011) PLoS Biol , vol.9
    • Philippe, H.1
  • 41
    • 53749090508 scopus 로고    scopus 로고
    • Empirical profile mixture models for phylogenetic reconstruction
    • Quang le S, Gascuel O, Lartillot N. 2008. Empirical profile mixture models for phylogenetic reconstruction. Bioinformatics 24: 2317-2323.
    • (2008) Bioinformatics , vol.24 , pp. 2317-2323
    • Quang Le, S.1    Gascuel, O.2    Lartillot, N.3
  • 43
    • 84881138595 scopus 로고    scopus 로고
    • Insights into the phylogeny and coding potential of microbial dark matter
    • Rinke C, et al. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499: 431-437.
    • (2013) Nature , vol.499 , pp. 431-437
    • Rinke, C.1
  • 45
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 46
    • 0042902833 scopus 로고    scopus 로고
    • The COG database: An updated version includes eukaryotes
    • Tatusov RL, et al. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4: 41.
    • (2003) BMC Bioinformatics , vol.4 , pp. 41
    • Tatusov, R.L.1
  • 47
    • 84890355580 scopus 로고    scopus 로고
    • An archaeal origin of eukaryotes supports only two primary domains of life
    • Williams TA, Foster PG, Cox CJ, Embley TM. 2013. An archaeal origin of eukaryotes supports only two primary domains of life. Nature 504: 231-236.
    • (2013) Nature , vol.504 , pp. 231-236
    • Williams, T.A.1    Foster, P.G.2    Cox, C.J.3    Embley, T.M.4
  • 48
  • 49
    • 0025300402 scopus 로고
    • Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya
    • Woese CR, Kandler O, Wheelis ML. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 87: 4576-4579.
    • (1990) Proc Natl Acad Sci U S A. , vol.87 , pp. 4576-4579
    • Woese, C.R.1    Kandler, O.2    Wheelis, M.L.3
  • 50
    • 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


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