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Volumn 33, Issue 7, 2016, Pages 1843-1857

Estimating the Frequency of Horizontal Gene Transfer Using Phylogenetic Models of Gene Gain and Loss

Author keywords

Archaea; Bacterial genomes; Cyanobacteria; Horizontal gene transfer; Phylogenetics

Indexed keywords

ARCHAEON; ARTICLE; BACTERIAL GENOME; CYANOBACTERIUM; GENE FREQUENCY; HORIZONTAL GENE TRANSFER; INHERITANCE; LOSS OF FUNCTION MUTATION; MAXIMUM LIKELIHOOD METHOD; NONHUMAN; PHYLOGENY; ARCHAEAL GENOME; BACTERIAL GENE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER SIMULATION; DNA SEQUENCE; GENE DELETION; GENETICS; MOLECULAR EVOLUTION; PROCEDURES;

EID: 85019145778     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/MOLBEV/MSW062     Document Type: Article
Times cited : (27)

References (45)
  • 1
    • 84876053703 scopus 로고    scopus 로고
    • Information theory and an extension of the maximum likelihood principle
    • New York: Springer
    • Akaike H. 1998. Information theory and an extension of the maximum likelihood principle. Selected papers of Hirotugu Akaike. New York: Springer. p. 199–213.
    • (1998) Selected papers of Hirotugu Akaike , pp. 199-213
    • Akaike, H.1
  • 2
    • 1342309210 scopus 로고    scopus 로고
    • Parallel metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference
    • Altekar G, Dwarkadas S, Huelsenbeck JP, Ronquist F. 2004. Parallel metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20:407–415.
    • (2004) Bioinformatics , vol.20 , pp. 407-415
    • Altekar, G1    Dwarkadas, S2    Huelsenbeck, JP3    Ronquist, F.4
  • 4
    • 77957711376 scopus 로고    scopus 로고
    • The diversity of a distributed genome in bacterial populations
    • Baumdicker F, Hess WR, Pfaffelhuber P. 2010. The diversity of a distributed genome in bacterial populations. Ann Appl Probab. 20:1567–1606.
    • (2010) Ann Appl Probab , vol.20 , pp. 1567-1606
    • Baumdicker, F1    Hess, WR2    Pfaffelhuber, P.3
  • 5
    • 84864083035 scopus 로고    scopus 로고
    • The infinitely many genes model for the distributed genome of bacteria
    • Baumdicker F, Hess WR, Pfaffelhuber P. 2012. The infinitely many genes model for the distributed genome of bacteria. Genome Biol Evol. 4:443–456.
    • (2012) Genome Biol Evol , vol.4 , pp. 443-456
    • Baumdicker, F1    Hess, WR2    Pfaffelhuber, P.3
  • 6
    • 84919828117 scopus 로고    scopus 로고
    • The infinitely many genes model with horizontal gene transfer
    • Baumdicker F, Pfaffelhuber P. 2014. The infinitely many genes model with horizontal gene transfer. Electron J Probab. 19:1–27.
    • (2014) Electron J Probab , vol.19 , pp. 1-27
    • Baumdicker, F1    Pfaffelhuber, P.2
  • 7
    • 33644700003 scopus 로고    scopus 로고
    • Toward automatic reconstruction of a highly resolved tree of life
    • Ciccarelli FD, Doerks T, Von Mering C, Creevey CJ, Snel B, Bork P. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283–1287.
    • (2006) Science , vol.311 , pp. 1283-1287
    • Ciccarelli, FD1    Doerks, T2    Von Mering, C3    Creevey, CJ4    Snel, B5    Bork, P.6
  • 8
    • 77249088623 scopus 로고    scopus 로고
    • Inference and characterization of horizontally transferred gene families using stochastic mapping
    • Cohen O, Pupko T. 2010. Inference and characterization of horizontally transferred gene families using stochastic mapping. Mol Biol Evol. 27:703–713.
    • (2010) Mol Biol Evol , vol.27 , pp. 703-713
    • Cohen, O1    Pupko, T.2
  • 10
    • 84867822025 scopus 로고    scopus 로고
    • Testing the infinitely many genes model for the evolution of the bacterial core genome and pangenome
    • Collins RE, Higgs PG. 2012. Testing the infinitely many genes model for the evolution of the bacterial core genome and pangenome. Mol Biol Evol. 29:3413–3425.
    • (2012) Mol Biol Evol , vol.29 , pp. 3413-3425
    • Collins, RE1    Higgs, PG.2
  • 11
    • 68949207909 scopus 로고    scopus 로고
    • Streamlining and large ancestral genomes in archaea inferred with a phylogenetic birth-and-death model
    • Csuros M, Miklos I. 2009. Streamlining and large ancestral genomes in archaea inferred with a phylogenetic birth-and-death model. Mol Biol Evol. 26:2087–2095.
    • (2009) Mol Biol Evol , vol.26 , pp. 2087-2095
    • Csuros, M1    Miklos, I.2
  • 12
    • 48249151749 scopus 로고    scopus 로고
    • Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution
    • Dagan T, Artzy-Randrup Y, Martin W. 2008. Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc Natl Acad Sci U S A. 105:10039–10044.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 10039-10044
    • Dagan, T1    Artzy-Randrup, Y2    Martin, W.3
  • 13
    • 33846476262 scopus 로고    scopus 로고
    • Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution
    • Dagan T, Martin W. 2007. Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution. Proc Natl Acad Sci U S A. 104:870–875.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 870-875
    • Dagan, T1    Martin, W.2
  • 15
    • 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
  • 16
    • 0031829758 scopus 로고    scopus 로고
    • Inferring pattern and process: maximum likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phyogentic analysis
    • Galtier N, Gouy M. 1998. Inferring pattern and process: maximum likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phyogentic analysis. Mol Biol Evol. 15:771–879.
    • (1998) Mol Biol Evol , vol.15 , pp. 771-879
    • Galtier, N1    Gouy, M.2
  • 17
    • 34247236709 scopus 로고    scopus 로고
    • Phylogenomic analysis of proteins that are distinctive of archaea and its main subgroups and the origin of methanogenesis
    • Gao B, Gupta RS. 2007. Phylogenomic analysis of proteins that are distinctive of archaea and its main subgroups and the origin of methanogenesis. BMC Genomics 8:86.
    • (2007) BMC Genomics , vol.8 , pp. 86
    • Gao, B1    Gupta, RS.2
  • 18
    • 26444580130 scopus 로고    scopus 로고
    • The cobweb of life revealed by genome-scale estimates of horizontal gene transfer
    • Ge F, Wang LS, Kim J. 2005. The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol. 3:e316.
    • (2005) PLoS Biol , vol.3 , pp. e316
    • Ge, F1    Wang, LS2    Kim, J.3
  • 19
    • 23944499633 scopus 로고    scopus 로고
    • Horizontal gene transfer, genome innovation and evolution
    • Gogarten JP, Townsend JP. 2005. Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol. 3:679–687.
    • (2005) Nat Rev Microbiol , vol.3 , pp. 679-687
    • Gogarten, JP1    Townsend, JP.2
  • 20
    • 77149149384 scopus 로고    scopus 로고
    • Signature proteins for the major clades of cyanobacteria
    • Gupta RS, Mathews DW. 2010. Signature proteins for the major clades of cyanobacteria. BMC Evol Biol. 10:24.
    • (2010) BMC Evol Biol , vol.10 , pp. 24
    • Gupta, RS1    Mathews, DW.2
  • 21
    • 33745172155 scopus 로고    scopus 로고
    • The fate of laterally transferred genes: life in the fast lane to adaptation or death
    • Hao W, Golding GB. 2006. The fate of laterally transferred genes: life in the fast lane to adaptation or death. Genome Res. 16:636–643.
    • (2006) Genome Res , vol.16 , pp. 636-643
    • Hao, W1    Golding, GB.2
  • 22
    • 84926099013 scopus 로고    scopus 로고
    • Phylogenetic analysis and molecular signatures defining a monophyletic clade of heterocystous cyanobacteria and identifying its closest relatives
    • Howard-Azzeh M, Shamseer L, Schellhorn HE, Gupta RS. 2014. Phylogenetic analysis and molecular signatures defining a monophyletic clade of heterocystous cyanobacteria and identifying its closest relatives. Photosynth Res. 122:171–185.
    • (2014) Photosynth Res , vol.122 , pp. 171-185
    • Howard-Azzeh, M1    Shamseer, L2    Schellhorn, HE3    Gupta, RS.4
  • 23
    • 84890379001 scopus 로고    scopus 로고
    • Models of gene gain and gene loss for probabilistic reconstruction of gene content in the last universal common ancestor of life
    • Kannan L, Li H, Rubinstein B, Mushegian A. 2013. Models of gene gain and gene loss for probabilistic reconstruction of gene content in the last universal common ancestor of life. Biol Direct 8:1–12.
    • (2013) Biol Direct , vol.8 , pp. 1-12
    • Kannan, L1    Li, H2    Rubinstein, B3    Mushegian, A.4
  • 24
    • 84877267452 scopus 로고    scopus 로고
    • Evolution of microbes and viruses: a paradigm shift in evolutionary biology?
    • Koonin EV, Wolf YI. 2012. Evolution of microbes and viruses: a paradigm shift in evolutionary biology? Front Cell Infect Microbiol. 2:119.
    • (2012) Front Cell Infect Microbiol , vol.2 , pp. 119
    • Koonin, EV1    Wolf, YI.2
  • 25
    • 22244450083 scopus 로고    scopus 로고
    • The net of life: reconstructing the microbial phylogenetic network
    • Kunin V, Goldovsky L, Darzentas N, Ouzounis CA. 2005. The net of life: reconstructing the microbial phylogenetic network. Genome Res. 15:954–959.
    • (2005) Genome Res , vol.15 , pp. 954-959
    • Kunin, V1    Goldovsky, L2    Darzentas, N3    Ouzounis, CA.4
  • 27
    • 61349194462 scopus 로고    scopus 로고
    • Estimating the size of the bacterial pangenome
    • Lapierre P, Gogarten JP. 2009. Estimating the size of the bacterial pangenome. Trends Genet. 25:107–110.
    • (2009) Trends Genet , vol.25 , pp. 107-110
    • Lapierre, P1    Gogarten, JP.2
  • 28
    • 84876523152 scopus 로고    scopus 로고
    • Gene frequency distributions reject a neutral model of genome evolution
    • Lobkovsky AE, Wolf YI, Koonin EV. 2013. Gene frequency distributions reject a neutral model of genome evolution. Genome Biol Evol. 5:233–242.
    • (2013) Genome Biol Evol , vol.5 , pp. 233-242
    • Lobkovsky, AE1    Wolf, YI2    Koonin, EV.3
  • 30
    • 2942622384 scopus 로고    scopus 로고
    • Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in
    • Mirkin BG, Fenner TI, Galperin MY, Koonin EV. 2003. Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in. BMC Evol Biol. 3:2.
    • (2003) BMC Evol Biol , vol.3 , pp. 2
    • Mirkin, BG1    Fenner, TI2    Galperin, MY3    Koonin, EV.4
  • 33
    • 68149093715 scopus 로고    scopus 로고
    • Search for a ‘Tree of Life’ in the thicket of the phylogenetic forest
    • Puigbo P, Wolf YI, Koonin EV. 2009. Search for a ‘Tree of Life’ in the thicket of the phylogenetic forest. J Biol. 8:59.
    • (2009) J Biol , vol.8 , pp. 59
    • Puigbo, P1    Wolf, YI2    Koonin, EV.3
  • 37
    • 0032900532 scopus 로고    scopus 로고
    • Genome phylogeny based on gene content
    • Snel B, Bork P, Huynen MA. 1999. Genome phylogeny based on gene content. Nat Genet. 21:108–110.
    • (1999) Nat Genet , vol.21 , pp. 108-110
    • Snel, B1    Bork, P2    Huynen, MA.3
  • 38
    • 67749145407 scopus 로고    scopus 로고
    • A phylogenetic mixture model for gene family loss in parasitic bacteria
    • Spencer M, Sangaralingam A. 2009. A phylogenetic mixture model for gene family loss in parasitic bacteria. Mol Biol Evol. 26:1901–1908.
    • (2009) Mol Biol Evol , vol.26 , pp. 1901-1908
    • Spencer, M1    Sangaralingam, A.2
  • 41
    • 0035031966 scopus 로고    scopus 로고
    • A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    • Whelan S, Goldman N. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol. 18:691–699.
    • (2001) Mol Biol Evol , vol.18 , pp. 691-699
    • Whelan, S1    Goldman, N.2
  • 42
    • 84881612486 scopus 로고    scopus 로고
    • Genome reduction as the dominant mode of evolution
    • Wolf YI, Koonin EV. 2013. Genome reduction as the dominant mode of evolution. Bioessays 35:829–837.
    • (2013) Bioessays , vol.35 , pp. 829-837
    • Wolf, YI1    Koonin, EV.2
  • 43
    • 84870950237 scopus 로고    scopus 로고
    • Updated clusters of orthologous genes for archaea: a complex ancestor of the archaea and the byways of horizontal gene transfer
    • Wolf YI, Makarova KS, Yutin N, Koonin EV. 2012. Updated clusters of orthologous genes for archaea: a complex ancestor of the archaea and the byways of horizontal gene transfer. Biol Direct. 7:46.
    • (2012) Biol Direct , vol.7 , pp. 46
    • Wolf, YI1    Makarova, KS2    Yutin, N3    Koonin, EV.4
  • 44
    • 0027132974 scopus 로고
    • Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
    • Yang Z. 1993. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol. 10:1396–1401.
    • (1993) Mol Biol Evol , vol.10 , pp. 1396-1401
    • Yang, Z.1
  • 45
    • 33748277982 scopus 로고    scopus 로고
    • Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events
    • Zhaxybayeva O, Gogarten JP, Charlebois RL, Doolittle WF, Papke RT. 2006. Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Res. 16:1099–1108.
    • (2006) Genome Res , vol.16 , pp. 1099-1108
    • Zhaxybayeva, O1    Gogarten, JP2    Charlebois, RL3    Doolittle, WF4    Papke, RT.5


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