메뉴 건너뛰기




Volumn 7262 LNBI, Issue , 2012, Pages 224-238

Recovering the tree-like trend of evolution despite extensive lateral genetic transfer: A probabilistic analysis

Author keywords

Lateral Gene Transfer; Phylogenetic Reconstruction; Quartet Reconstruction

Indexed keywords

ADAPTIVE EVOLUTION; COMPUTATIONALLY EFFICIENT; EVOLUTIONARY HISTORY; GENE TREE; GENETIC MATERIALS; PHYLOGENETIC RECONSTRUCTION; PROBABILISTIC ANALYSIS; RANDOMLY DISTRIBUTED; TREE OF LIFE;

EID: 84860820866     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-29627-7_23     Document Type: Conference Paper
Times cited : (11)

References (53)
  • 1
    • 70349414048 scopus 로고    scopus 로고
    • The gene evolution model and computing its associated probabilities
    • [ALS09]
    • [ALS09] Arvestad, L., Lagergren, J., Sennblad, B.: The gene evolution model and computing its associated probabilities. J. ACM 56(2) (2009)
    • (2009) J. ACM , vol.56 , Issue.2
    • Arvestad, L.1    Lagergren, J.2    Sennblad, B.3
  • 2
    • 0002844544 scopus 로고
    • Combining trees as a way of combining data sets for phylogenetic inference
    • [Bau92]
    • [Bau92] Baum, B.R.: Combining trees as a way of combining data sets for phylogenetic inference. Taxon 41, 3-10 (1992)
    • (1992) Taxon , vol.41 , pp. 3-10
    • Baum, B.R.1
  • 5
    • 0001117764 scopus 로고    scopus 로고
    • Inferring evolutionary trees with strong combinatorial evidence
    • [BG01]
    • [BG01] Berry, V., Gascuel, O.: Inferring evolutionary trees with strong combinatorial evidence. Theoretical Computer Science (240), 271-298 (2001)
    • (2001) Theoretical Computer Science , vol.240 , pp. 271-298
    • Berry, V.1    Gascuel, O.2
  • 8
    • 0002074731 scopus 로고
    • The recovery of trees from measures of dissimilarity
    • [Bun71]. Edinburgh University Press, Mamaia Hodson, F.R., Kendall, D.G., Tautu, P. (eds
    • [Bun71] Buneman, P.: The recovery of trees from measures of dissimilarity. In: Hodson, F.R., Kendall, D.G., Tautu, P. (eds.) Anglo-Romanian Conference on Mathematics in the Archaeological and Historical Sciences, pp. 387-395. Edinburgh University Press, Mamaia (1971)
    • (1971) Anglo-Romanian Conference on Mathematics in the Archaeological and Historical Sciences , pp. 387-395
    • Buneman, P.1
  • 9
    • 79955380843 scopus 로고    scopus 로고
    • Comparing two bayesian methods for gene tree/species tree reconstruction: Simulations with incomplete lineage sorting and horizontal gene transfer
    • [CA11]
    • [CA11] Chung, Y., Ane, C.: Comparing two bayesian methods for gene tree/species tree reconstruction: Simulations with incomplete lineage sorting and horizontal gene transfer. Systematic Biology 60(3), 261-275 (2011)
    • (2011) Systematic Biology , vol.60 , Issue.3 , pp. 261-275
    • Chung, Y.1    Ane, C.2
  • 10
    • 33745796718 scopus 로고    scopus 로고
    • A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer
    • [CM06] , Apostolico, A., Guerra, C., Istrail, S., Pevzner, P.A., Waterman, M. (eds.), Springer, Heidelberg
    • [CM06] Csřös, M., Miklós, I.: A Probabilistic Model for Gene Content Evolution with Duplication, Loss, and Horizontal Transfer. In: Apostolico, A., Guerra, C., Istrail, S., Pevzner, P.A., Waterman, M. (eds.) RECOMB 2006. LNCS (LNBI), vol. 3909, pp. 206-220. Springer, Heidelberg (2006)
    • (2006) RECOMB 2006. LNCS (LNBI) , vol.3909 , pp. 206-220
    • Csřös, M.1    Miklós, I.2
  • 11
    • 33847790997 scopus 로고    scopus 로고
    • Pattern pluralism and the tree of life hypothesis
    • [DB07]
    • [DB07] Doolittle, W.F., Bapteste, E.: Pattern pluralism and the tree of life hypothesis. Proc. Natl. Acad. Sci. USA 104, 2043-2049 (2007)
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 2043-2049
    • Doolittle, W.F.1    Bapteste, E.2
  • 12
    • 17744394753 scopus 로고    scopus 로고
    • Phylogenomics and the reconstruction of the tree of life
    • [DBP05]
    • [DBP05] Delsuc, F., Brinkmann, H., Philippe, H.: Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet. 6(5), 361-375 (2005)
    • (2005) Nat. Rev. Genet. , vol.6 , Issue.5 , pp. 361-375
    • Delsuc, F.1    Brinkmann, H.2    Philippe, H.3
  • 13
    • 33750810896 scopus 로고    scopus 로고
    • The tree of one percent
    • [DM06]
    • [DM06] Dagan, T., Martin, W.: The tree of one percent. Genome Biology 7(10), 118 (2006)
    • (2006) Genome Biology , vol.7 , Issue.10 , pp. 118
    • Dagan, T.1    Martin, W.2
  • 14
    • 79952002699 scopus 로고    scopus 로고
    • Evolutionary trees and the ising model on the bethe lattice: A proof of steel's conjecture
    • [DMR11], doi:10.1007/s00440-009-0246-2
    • [DMR11] Daskalakis, C., Mossel, E., Roch, S.: Evolutionary trees and the ising model on the bethe lattice: A proof of steel's conjecture. Probability Theory and Related Fields 149, 149-189 (2011), doi:10.1007/s00440-009-0246-2
    • (2011) Probability Theory and Related Fields , vol.149 , pp. 149-189
    • Daskalakis, C.1    Mossel, E.2    Roch, S.3
  • 15
    • 65649131928 scopus 로고    scopus 로고
    • Gene tree discordance, phylogenetic inference and themultispecies coalescent
    • [DR09]
    • [DR09] Degnan, J.H., Rosenberg, N.A.: Gene tree discordance, phylogenetic inference and themultispecies coalescent. Trends in Ecology and Evolution 24(6), 332-340 (2009)
    • (2009) Trends in Ecology and Evolution , vol.24 , Issue.6 , pp. 332-340
    • Degnan, J.H.1    Rosenberg, N.A.2
  • 16
    • 78650257028 scopus 로고    scopus 로고
    • Alignment-free phylogenetic reconstruction
    • [DR10], Berger, B. (ed.), Springer, Heidelberg
    • [DR10] Daskalakis, C., Roch, S.: Alignment-Free Phylogenetic Reconstruction. In: Berger, B. (ed.) RECOMB 2010. LNCS, vol. 6044, pp. 123-137. Springer, Heidelberg (2010)
    • (2010) RECOMB 2010. LNCS , vol.6044 , pp. 123-137
    • Daskalakis, C.1    Roch, S.2
  • 17
    • 24344510265 scopus 로고    scopus 로고
    • Discordant 16S and 23S rRNA gene phylogenies for the Genus Helicobacter: Implications for phylogenetic inference and systematics
    • [DSS+05]
    • [DSS+05] Dewhirst, F.E., Shen, Z., Scimeca, M.S., Stokes, L.N., Boumenna, T., Chen, T., Paster, B.J., Fox, J.G.: Discordant 16S and 23S rRNA gene phylogenies for the Genus Helicobacter: Implications for phylogenetic inference and systematics. J. Bacteriol. 187(17), 6106-6118 (2005)
    • (2005) J. Bacteriol. , vol.187 , Issue.17 , pp. 6106-6118
    • Dewhirst, F.E.1    Shen, Z.2    Scimeca, M.S.3    Stokes, L.N.4    Boumenna, T.5    Chen, T.6    Paster, B.J.7    Fox, J.G.8
  • 18
    • 0038518196 scopus 로고    scopus 로고
    • Phylogenomics: Intersection of evolution and genomics
    • [EF03]
    • [EF03] Eisen, J.A., Fraser, C.M.: Phylogenomics: Intersection of evolution and genomics. Science 300(5626), 1706-1707 (2003)
    • (2003) Science , vol.300 , Issue.5626 , pp. 1706-1707
    • Eisen, J.A.1    Fraser, C.M.2
  • 19
    • 38449096427 scopus 로고    scopus 로고
    • A model of horizontal gene transfer and the bacterial phylogeny problem
    • [Gal07]
    • [Gal07] Galtier, N.: A model of horizontal gene transfer and the bacterial phylogeny problem. Systematic Biology 56(4), 633-642 (2007)
    • (2007) Systematic Biology , vol.56 , Issue.4 , pp. 633-642
    • Galtier, N.1
  • 20
    • 57149095052 scopus 로고    scopus 로고
    • Dealing with incongruence in phylogenomic analyses
    • [GD08]
    • [GD08] Galtier, N., Daubin, V.: Dealing with incongruence in phylogenomic analyses. Philos. Trans. R Soc. Lond. B Biol. Sci. 363, 4023-4029 (2008)
    • (2008) Philos. Trans. R Soc. Lond. B Biol. Sci. , vol.363 , pp. 4023-4029
    • Galtier, N.1    Daubin, V.2
  • 22
    • 23944499633 scopus 로고    scopus 로고
    • Horizontal gene transfer, genome innovation and evolution
    • [GT05]
    • [GT05] Peter Gogarten, J., Townsend, J.P.: Horizontal gene transfer, genome innovation and evolution. Nat. Rev. Micro. 3(9), 679-687 (2005)
    • (2005) Nat. Rev. Micro. , vol.3 , Issue.9 , pp. 679-687
    • Peter Gogarten, J.1    Townsend, J.P.2
  • 23
    • 26444580130 scopus 로고    scopus 로고
    • The cobweb of life revealed by genome-scale estimates of horizontal gene transfer
    • [GWK05]
    • [GWK05] Ge, F., Wang, L.S., Kim, J.: The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol. 3, e316 (2005)
    • (2005) PLoS Biol. , vol.3
    • Ge, F.1    Wang, L.S.2    Kim, J.3
  • 25
    • 70149100417 scopus 로고    scopus 로고
    • A statistical approach for distinguishing hybridization and incomplete lineage sorting
    • [JML09]
    • [JML09] Joly, S., McLenachan, P.A., Lockhart, P.J.: A statistical approach for distinguishing hybridization and incomplete lineage sorting. The American Naturalist 174(2), E54-E70 (2009)
    • (2009) The American Naturalist , vol.174 , Issue.2
    • Joly, S.1    McLenachan, P.A.2    Lockhart, P.J.3
  • 26
    • 33750418625 scopus 로고    scopus 로고
    • Maximum likelihood of phylogenetic networks
    • [JNST06]
    • [JNST06] Jin, G., Nakhleh, L., Snir, S., Tuller, T.: Maximum likelihood of phylogenetic networks. Bioinformatics 22(21), 2604-2611 (2006)
    • (2006) Bioinformatics , vol.22 , Issue.21 , pp. 2604-2611
    • Jin, G.1    Nakhleh, L.2    Snir, S.3    Tuller, T.4
  • 27
    • 68649084421 scopus 로고    scopus 로고
    • Parsimony score of phylogenetic networks: Hardness results and a linear-time heuristic
    • [JNST09]
    • [JNST09] Jin, G., Nakhleh, L., Snir, S., Tuller, T.: Parsimony score of phylogenetic networks: Hardness results and a linear-time heuristic. IEEE/ACM Trans. Comput. Biology Bioinform. 6(3), 495-505 (2009)
    • (2009) IEEE/ACM Trans. Comput. Biology Bioinform. , vol.6 , Issue.3 , pp. 495-505
    • Jin, G.1    Nakhleh, L.2    Snir, S.3    Tuller, T.4
  • 28
    • 34548646673 scopus 로고    scopus 로고
    • The biological big bang model for the major transitions in evolution
    • [Koo07]
    • [Koo07] Koonin, E.V.: The biological big bang model for the major transitions in evolution. Biol. Direct. 2, 21 (2007)
    • (2007) Biol. Direct. , vol.2 , pp. 21
    • Koonin, E.V.1
  • 29
    • 79959849261 scopus 로고    scopus 로고
    • Comparison of phylogenetic trees and search for a central trend in the forest of life
    • [KPW11]
    • [KPW11] Koonin, E.V., Puigbo, P., Wolf, Y.I.: Comparison of phylogenetic trees and search for a central trend in the forest of life. Journal of Computational Biology 18(7), 917-924 (2011)
    • (2011) Journal of Computational Biology , vol.18 , Issue.7 , pp. 917-924
    • Koonin, E.V.1    Puigbo, P.2    Wolf, Y.I.3
  • 30
    • 0035222177 scopus 로고    scopus 로고
    • A tree obscured by vines: Horizontal gene transfer and the median tree method of estimating species phylogeny
    • [KS01]
    • [KS01] Kim, J., Salisbury, B.A.: A tree obscured by vines: Horizontal gene transfer and the median tree method of estimating species phylogeny. In: Pacific Symposium on Biocomputing, pp. 571-582 (2001)
    • (2001) Pacific Symposium on Biocomputing , pp. 571-582
    • Kim, J.1    Salisbury, B.A.2
  • 31
    • 70450277249 scopus 로고    scopus 로고
    • Identifying hybridization events in the presence of coalescence via model selection
    • [Kub09]
    • [Kub09] Kubatko, L.S.: Identifying hybridization events in the presence of coalescence via model selection. Systematic Biology 58(5), 478-488 (2009)
    • (2009) Systematic Biology , vol.58 , Issue.5 , pp. 478-488
    • Kubatko, L.S.1
  • 33
    • 0031504952 scopus 로고    scopus 로고
    • Gene trees in species trees
    • [Mad97]
    • [Mad97] Maddison, W.P.: Gene trees in species trees. Systematic Biology 46(3), 523-536 (1997)
    • (1997) Systematic Biology , vol.46 , Issue.3 , pp. 523-536
    • Maddison, W.P.1
  • 34
    • 58249136809 scopus 로고    scopus 로고
    • Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model
    • [MK09]
    • [MK09] Meng, C., Kubatko, L.S.: Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model. Theoretical Population Biology 75(1), 35-45 (2009)
    • (2009) Theoretical Population Biology , vol.75 , Issue.1 , pp. 35-45
    • Meng, C.1    Kubatko, L.S.2
  • 35
    • 2442663027 scopus 로고    scopus 로고
    • Phase transitions in phylogeny
    • [Mos04]
    • [Mos04] Mossel, E.: Phase transitions in phylogeny. Trans. Amer. Math. Soc. 356(6), 2379-2404 (2004)
    • (2004) Trans. Amer. Math. Soc. , vol.356 , Issue.6 , pp. 2379-2404
    • Mossel, E.1
  • 36
    • 68149093715 scopus 로고    scopus 로고
    • Search for a 'tree of life' in the thicket of the phylogenetic forest
    • [PWK09]
    • [PWK09] Puigbo, P., Wolf, Y., Koonin, E.: Search for a 'tree of life' in the thicket of the phylogenetic forest. Journal of Biology 8(6), 59 (2009)
    • (2009) Journal of Biology , vol.8 , Issue.6 , pp. 59
    • Puigbo, P.1    Wolf, Y.2    Koonin, E.3
  • 37
    • 79952201675 scopus 로고    scopus 로고
    • The tree and net components of prokaryote evolution
    • [PWK10]
    • [PWK10] Puigbo, P., Wolf, Y.I., Koonin, E.V.: The tree and net components of prokaryote evolution. Genome Biology and Evolution 2, 745-756 (2010)
    • (2010) Genome Biology and Evolution , vol.2 , pp. 745-756
    • Puigbo, P.1    Wolf, Y.I.2    Koonin, E.V.3
  • 38
    • 0027104018 scopus 로고
    • Matrix representation in reconstructing phylogeneticrelationships among the eukaryotes
    • [Rag92]
    • [Rag92] Ragan, M.A.: Matrix representation in reconstructing phylogeneticrelationships among the eukaryotes. Biosystems 28, 47-55 (1992)
    • (1992) Biosystems , vol.28 , pp. 47-55
    • Ragan, M.A.1
  • 40
    • 0029818407 scopus 로고    scopus 로고
    • Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference
    • [RY96]
    • [RY96] Rannala, B., Yang, Z.: Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference. J. Mol. Evol. 43, 304-311 (1996)
    • (1996) J. Mol. Evol. , vol.43 , pp. 304-311
    • Rannala, B.1    Yang, Z.2
  • 41
    • 23944441749 scopus 로고    scopus 로고
    • Horizontal gene transfer: Perspectives at a crossroads of scientific disciplines
    • [SB05]
    • [SB05] Smets, B.F., Barkay, T.: Horizontal gene transfer: Perspectives at a crossroads of scientific disciplines. Nat. Rev. Micro. 3(9), 675-678 (2005)
    • (2005) Nat. Rev. Micro. , vol.3 , Issue.9 , pp. 675-678
    • Smets, B.F.1    Barkay, T.2
  • 42
    • 78149235569 scopus 로고    scopus 로고
    • Quartetsmaxcut: Adivide and conquer quartets algorithm
    • [SR10]
    • [SR10] Snir, S., Rao, S.: Quartetsmaxcut: Adivide and conquer quartets algorithm. IEEE/ACM Trans. Comput. Biology Bioinform. 7(4), 704-718 (2010)
    • (2010) IEEE/ACM Trans. Comput. Biology Bioinform. , vol.7 , Issue.4 , pp. 704-718
    • Snir, S.1    Rao, S.2
  • 43
    • 83655184666 scopus 로고    scopus 로고
    • Quartet maxcut: A fast algorithm for amalgamating quartet trees
    • [SR12]
    • [SR12] Snir, S., Rao, S.: Quartet maxcut: A fast algorithm for amalgamating quartet trees. Molecular Phylogenetics and Evolution 62(1), 1-8 (2012)
    • (2012) Molecular Phylogenetics and Evolution , vol.62 , Issue.1 , pp. 1-8
    • Snir, S.1    Rao, S.2
  • 45
    • 0344666688 scopus 로고    scopus 로고
    • Horizontal transfer of segments of the 16S rRNA genes between species of the Streptococcus anginosus group
    • [SSJ03]
    • [SSJ03] Schouls, L.M., Schot, C.S., Jacobs, J.A.: Horizontal transfer of segments of the 16S rRNA genes between species of the Streptococcus anginosus group. J. Bacteriol. 185(24), 7241-7246 (2003)
    • (2003) J. Bacteriol. , vol.185 , Issue.24 , pp. 7241-7246
    • Schouls, L.M.1    Schot, C.S.2    Jacobs, J.A.3
  • 46
    • 52449147252 scopus 로고
    • The complexity of reconstructing trees from qualitative characters and subtress
    • [Ste92]
    • [Ste92] Steel, M.: The complexity of reconstructing trees from qualitative characters and subtress. Journal of Classification 9(1), 91-116 (1992)
    • (1992) Journal of Classification , vol.9 , Issue.1 , pp. 91-116
    • Steel, M.1
  • 47
    • 20444410815 scopus 로고    scopus 로고
    • Stochastic models for horizontal gene transfer
    • [Suc05]
    • [Suc05] Suchard, M.A.: Stochastic models for horizontal gene transfer. Genetics 170(1), 419-431 (2005)
    • (2005) Genetics , vol.170 , Issue.1 , pp. 419-431
    • Suchard, M.A.1
  • 48
    • 34250380386 scopus 로고    scopus 로고
    • Confounding factors in hgt detection: Statistical error, coalescent effects, and multiple solutions
    • [TRIN07]
    • [TRIN07] Than, C., Ruths, D., Innan, H., Nakhleh, L.: Confounding factors in hgt detection: Statistical error, coalescent effects, and multiple solutions. Journal of Computational Biology 14(4), 517-535 (2007)
    • (2007) Journal of Computational Biology , vol.14 , Issue.4 , pp. 517-535
    • Than, C.1    Ruths, D.2    Innan, H.3    Nakhleh, L.4
  • 50
    • 79951575208 scopus 로고    scopus 로고
    • Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting
    • [YTDN11]
    • [YTDN11] Yu, Y., Than, C., Degnan, J.H., Nakhleh, L.: Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting. Systematic Biology 60(2), 138-149 (2011)
    • (2011) Systematic Biology , vol.60 , Issue.2 , pp. 138-149
    • Yu, Y.1    Than, C.2    Degnan, J.H.3    Nakhleh, L.4
  • 51
    • 0032835111 scopus 로고    scopus 로고
    • Distinct types of rrna operons exist in the genome of the Actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon
    • [YZW99]
    • [YZW99] Yap, W.H., Zhang, Z., Wang, Y.: Distinct types of rrna operons exist in the genome of the Actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon. J. Bacteriol. 181(17), 5201-5209 (1999)
    • (1999) J. Bacteriol. , vol.181 , Issue.17 , pp. 5201-5209
    • Yap, W.H.1    Zhang, Z.2    Wang, Y.3
  • 52
    • 33748277982 scopus 로고    scopus 로고
    • Phylogenetic analyses of cyanobacterial genomes:Quantification of horizontal gene transfer events
    • [ZGC+06]
    • [ZGC+06] Zhaxybayeva, O., Peter Gogarten, J., Charlebois, R.L., Ford Doolittle, W., ThanePapke,R.:Phylogenetic analyses of cyanobacterial genomes:Quantification of horizontal gene transfer events.Genome Research 16(9), 1099-1108 (2006)
    • (2006) Genome Research , vol.16 , Issue.9 , pp. 1099-1108
    • Zhaxybayeva, O.1    Peter Gogarten, J.2    Charlebois, R.L.3    Ford Doolittle, W.4    ThanePapke, R.5
  • 53
    • 1942422301 scopus 로고    scopus 로고
    • Genome mosaicism and organismal lineages
    • [ZLG04]
    • [ZLG04] Zhaxybayeva, O., Lapierre, P., Gogarten, J.P.: Genome mosaicism and organismal lineages. Trends Genet 20, 254-260 (2004)
    • (2004) Trends Genet , vol.20 , pp. 254-260
    • Zhaxybayeva, O.1    Lapierre, P.2    Gogarten, J.P.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.