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Volumn 322, Issue , 2013, Pages 81-93

Identifying a species tree subject to random lateral gene transfer

Author keywords

Modeling LGT; Phylogenetic tree; Poisson process; Statistical consistency

Indexed keywords

DATA SET; GENE TRANSFER; PHYLOGENETICS; POISSON RATIO; STATISTICAL ANALYSIS; TREE;

EID: 84874438887     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2013.01.009     Document Type: Article
Times cited : (13)

References (41)
  • 1
    • 84859467874 scopus 로고    scopus 로고
    • Lateral gene transfer as a support for the Tree of Life
    • Abby S.S., Tannier E., Gouy M., Vincent D. Lateral gene transfer as a support for the Tree of Life. Proc. Natl. Acad. Sci. 2012, 109(13):4962-4967.
    • (2012) Proc. Natl. Acad. Sci. , vol.109 , Issue.13 , pp. 4962-4967
    • Abby, S.S.1    Tannier, E.2    Gouy, M.3    Vincent, D.4
  • 2
    • 80052517011 scopus 로고    scopus 로고
    • Determining species tree topologies from clade probabilities under the coalescent
    • Allman E.S., Degnan J.H., Rhodes J.A. Determining species tree topologies from clade probabilities under the coalescent. J. Theor. Biol. 2011, 289:96-106.
    • (2011) J. Theor. Biol. , vol.289 , pp. 96-106
    • Allman, E.S.1    Degnan, J.H.2    Rhodes, J.A.3
  • 4
    • 79959674740 scopus 로고    scopus 로고
    • Rooting phylogenies using gene duplications. an empirical example from the bees (Apoidea)
    • Brady S.G., Litman J.R., Danforth B.N. Rooting phylogenies using gene duplications. an empirical example from the bees (Apoidea). Mol. Phyl. Evol. 2011, 60:295-304.
    • (2011) Mol. Phyl. Evol. , vol.60 , pp. 295-304
    • Brady, S.G.1    Litman, J.R.2    Danforth, B.N.3
  • 5
    • 1642519173 scopus 로고    scopus 로고
    • A classification of consensus methods for phylogenies
    • American Mathematical Society, M. Janowitz, F.-J. Lapointe, F.R. McMorris, B. Mirkin, F.S. Roberts (Eds.)
    • Bryant D. A classification of consensus methods for phylogenies. BioConsensus. Providence (RI). Center for Discrete Mathematics and Theoretical Computer Science 2003, 163-183. American Mathematical Society. M. Janowitz, F.-J. Lapointe, F.R. McMorris, B. Mirkin, F.S. Roberts (Eds.).
    • (2003) BioConsensus. Providence (RI). Center for Discrete Mathematics and Theoretical Computer Science , pp. 163-183
    • Bryant, D.1
  • 6
    • 79955380843 scopus 로고    scopus 로고
    • Comparing two Bayesian methods for gene tree/species tree reconstruction. a simulation with incomplete lineage sorting and horizontal gene transfer
    • Chung Y., Ané C. Comparing two Bayesian methods for gene tree/species tree reconstruction. a simulation with incomplete lineage sorting and horizontal gene transfer. Syst. Biol. 2011, 60(3):261-275.
    • (2011) Syst. Biol. , vol.60 , Issue.3 , pp. 261-275
    • Chung, Y.1    Ané, C.2
  • 7
    • 70450231658 scopus 로고    scopus 로고
    • Species trees from highly incongruent gene trees in rice
    • Cranston K.A., Hurwitz B., Ware D., Stein L., Wing R.A. Species trees from highly incongruent gene trees in rice. Syst. Biol. 2009, 58(5):489-500.
    • (2009) Syst. Biol. , vol.58 , Issue.5 , pp. 489-500
    • Cranston, K.A.1    Hurwitz, B.2    Ware, D.3    Stein, L.4    Wing, R.A.5
  • 8
    • 33846476262 scopus 로고    scopus 로고
    • Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution
    • Dagan T., Martin W. Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution. Proc. Natl. Acad. Sci. USA 2007, 104(3):870-875.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , Issue.3 , pp. 870-875
    • Dagan, T.1    Martin, W.2
  • 9
    • 33750810896 scopus 로고    scopus 로고
    • The tree of one percent
    • Dagan T., Martin W. The tree of one percent. Genome Biol. 2006, 7(10):118.
    • (2006) Genome Biol. , vol.7 , Issue.10 , pp. 118
    • Dagan, T.1    Martin, W.2
  • 10
    • 67449167484 scopus 로고    scopus 로고
    • Properties of consensus methods for inferring species trees from gene trees
    • Degnan J., DeGiorgio M., Bryant D., Rosenberg N. Properties of consensus methods for inferring species trees from gene trees. Syst. Biol. 2009, 58:35-54.
    • (2009) Syst. Biol. , vol.58 , pp. 35-54
    • Degnan, J.1    DeGiorgio, M.2    Bryant, D.3    Rosenberg, N.4
  • 11
    • 0033603539 scopus 로고    scopus 로고
    • Phylogenetic classification and the universal tree
    • Doolittle W.F. Phylogenetic classification and the universal tree. Science 1999, 284(5423):2124-2129.
    • (1999) Science , vol.284 , Issue.5423 , pp. 2124-2129
    • Doolittle, W.F.1
  • 12
    • 0000472542 scopus 로고
    • Estimating phylogenetic trees from distance matrices
    • Farris J.S. Estimating phylogenetic trees from distance matrices. Am. Nat. 1972, 106:645-668.
    • (1972) Am. Nat. , vol.106 , pp. 645-668
    • Farris, J.S.1
  • 14
    • 38449096427 scopus 로고    scopus 로고
    • A model of horizontal gene transfer and the bacterial phylogeny problem
    • Galtier N. A model of horizontal gene transfer and the bacterial phylogeny problem. Syst. Biol. 2007, 56:633-642.
    • (2007) Syst. Biol. , vol.56 , pp. 633-642
    • Galtier, N.1
  • 15
    • 57149095052 scopus 로고    scopus 로고
    • Dealing with incongruence in phylogenomic analyses
    • Galtier N., Daubin V. Dealing with incongruence in phylogenomic analyses. Philos. Trans. R. Soc. Lond. (B) 2008, 363:4023-4029.
    • (2008) Philos. Trans. R. Soc. Lond. (B) , vol.363 , pp. 4023-4029
    • Galtier, N.1    Daubin, V.2
  • 17
    • 36849014457 scopus 로고    scopus 로고
    • An empirical test of the midpoint rooting method
    • Hess P.N., De Moraes Russo C.A. An empirical test of the midpoint rooting method. Biol. J. Linn. Soc. 2007, 92:669-674.
    • (2007) Biol. J. Linn. Soc. , vol.92 , pp. 669-674
    • Hess, P.N.1    De Moraes Russo, C.A.2
  • 18
    • 33847253862 scopus 로고    scopus 로고
    • Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model
    • Hobbolt A., Christensen O.F., Mailund T., Shierup M. Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLoS Genet. 2007, 3:e7.
    • (2007) PLoS Genet. , vol.3
    • Hobbolt, A.1    Christensen, O.F.2    Mailund, T.3    Shierup, M.4
  • 19
    • 0038632308 scopus 로고    scopus 로고
    • Outgroup misplacement and phylogenetic inaccuracy under a molecular clock-a simulation study
    • Holland B.R., Penny D., Hendy M.D. Outgroup misplacement and phylogenetic inaccuracy under a molecular clock-a simulation study. Syst. Biol. 2003, 52:229-238.
    • (2003) Syst. Biol. , vol.52 , pp. 229-238
    • Holland, B.R.1    Penny, D.2    Hendy, M.D.3
  • 20
    • 49249091441 scopus 로고    scopus 로고
    • The power of supernetworks to distinguish hybridisation from lineage-sorting via collections of gene trees
    • Holland B., Bentham S., Lockhart P., Moulton P., Huber K. The power of supernetworks to distinguish hybridisation from lineage-sorting via collections of gene trees. BMC Evol. Biol. 2008, 8:202.
    • (2008) BMC Evol. Biol. , vol.8 , pp. 202
    • Holland, B.1    Bentham, S.2    Lockhart, P.3    Moulton, P.4    Huber, K.5
  • 21
    • 0035527408 scopus 로고    scopus 로고
    • Difficulties in detecting hybridization
    • Holder M.T., Anderson J.A., Holloway A.K. Difficulties in detecting hybridization. Syst. Biol. 2001, 50(6):978-982.
    • (2001) Syst. Biol. , vol.50 , Issue.6 , pp. 978-982
    • Holder, M.T.1    Anderson, J.A.2    Holloway, A.K.3
  • 23
    • 84868007353 scopus 로고    scopus 로고
    • Dendroscope 3. an interactive tool for rooted phylogenetic trees and networks
    • Huson D.H., Scornavacca C. Dendroscope 3. an interactive tool for rooted phylogenetic trees and networks. Syst. Biol. 2012, 61(6):1061-1067.
    • (2012) Syst. Biol. , vol.61 , Issue.6 , pp. 1061-1067
    • Huson, D.H.1    Scornavacca, C.2
  • 24
    • 0033616714 scopus 로고    scopus 로고
    • Horizontal gene transfer among genomes. the complexity hypothesis
    • Jain R., Rivera M.C., Lake J.A. Horizontal gene transfer among genomes. the complexity hypothesis. Proc. Natl. Acad. Sci. USA 1999, 96(7):3801-3806.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , Issue.7 , pp. 3801-3806
    • Jain, R.1    Rivera, M.C.2    Lake, J.A.3
  • 25
    • 70149100417 scopus 로고    scopus 로고
    • A statistical approach for distinguishing hybridization and incomplete lineage sorting
    • Joly S., McLenachan P.A., Lockhart P.J. A statistical approach for distinguishing hybridization and incomplete lineage sorting. Am. Nat. 2009, 174(2):E54-E70.
    • (2009) Am. Nat. , vol.174 , Issue.2
    • Joly, S.1    McLenachan, P.A.2    Lockhart, P.J.3
  • 26
    • 34548081542 scopus 로고    scopus 로고
    • A likelihood framework to measure horizontal gene transfer
    • Linz S., Radtke A., von Haeseler A. A likelihood framework to measure horizontal gene transfer. Mol. Biol. Evol. 2007, 24(6):1312-1319.
    • (2007) Mol. Biol. Evol. , vol.24 , Issue.6 , pp. 1312-1319
    • Linz, S.1    Radtke, A.2    von Haeseler, A.3
  • 27
    • 84866512468 scopus 로고    scopus 로고
    • The impact and interplay of long and short branches on phylogenetic information content
    • Martyn I., Steel M. The impact and interplay of long and short branches on phylogenetic information content. J. Theor. Biol. 2012, 314:157-163.
    • (2012) J. Theor. Biol. , vol.314 , pp. 157-163
    • Martyn, I.1    Steel, M.2
  • 29
    • 33750437728 scopus 로고    scopus 로고
    • Widespread discordance of gene trees with species tree in Drosophila. evidence for incomplete lineage sorting
    • Pollard D.A., Iyer V.N., Moses A.M., Eisen M.B. Widespread discordance of gene trees with species tree in Drosophila. evidence for incomplete lineage sorting. PLoS Genet. 2006, 2:1634-1647.
    • (2006) PLoS Genet. , vol.2 , pp. 1634-1647
    • Pollard, D.A.1    Iyer, V.N.2    Moses, A.M.3    Eisen, M.B.4
  • 30
    • 84874406854 scopus 로고    scopus 로고
    • Recovering the tree-like trend of evolution despite extensive lateral genetic transfer: a probabilistic analysis
    • in press
    • Roch, S., Snir, S. Recovering the tree-like trend of evolution despite extensive lateral genetic transfer: a probabilistic analysis. J. Comput. Biol., in press, http://arXiv:1206.3520.
    • J. Comput. Biol.
    • Roch, S.1    Snir, S.2
  • 31
    • 0036515730 scopus 로고    scopus 로고
    • The probability of topological concordance of gene trees and species trees
    • Rosenberg N.A. The probability of topological concordance of gene trees and species trees. Theor. Pop. Biol. 2002, 61:225-247.
    • (2002) Theor. Pop. Biol. , vol.61 , pp. 225-247
    • Rosenberg, N.A.1
  • 32
    • 77952490857 scopus 로고    scopus 로고
    • Phylogenomics with incomplete taxon coverage. the limits to inference
    • Sanderson M.J., McMahon M.M., Steel M. Phylogenomics with incomplete taxon coverage. the limits to inference. BMC Evol. Biol. 2010, 10:155.
    • (2010) BMC Evol. Biol. , vol.10 , pp. 155
    • Sanderson, M.J.1    McMahon, M.M.2    Steel, M.3
  • 34
    • 77955928122 scopus 로고    scopus 로고
    • Expected length of pendant and interior edges of a Yule tree
    • Steel M., Mooers A. Expected length of pendant and interior edges of a Yule tree. Appl. Math. Lett. 2010, 23(11):1315-1319.
    • (2010) Appl. Math. Lett. , vol.23 , Issue.11 , pp. 1315-1319
    • Steel, M.1    Mooers, A.2
  • 35
    • 20444410815 scopus 로고    scopus 로고
    • Stochastic models for horizontal gene transfer. taking a random walk through tree space
    • Suchard M.A. Stochastic models for horizontal gene transfer. taking a random walk through tree space. Genetics 2005, 170:419-431.
    • (2005) Genetics , vol.170 , pp. 419-431
    • Suchard, M.A.1
  • 36
    • 84867904826 scopus 로고    scopus 로고
    • Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations
    • Szöllo G.J., Boussau B., Abby S.S., Tanniera E., Daubin V. Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations. Proc. Natl. Acad. Sci. USA 2012, 109(43):17513-17518.
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , Issue.43 , pp. 17513-17518
    • Szöllo, G.J.1    Boussau, B.2    Abby, S.S.3    Tanniera, E.4    Daubin, V.5
  • 37
    • 0021066244 scopus 로고
    • Evolutionary relationships of DNA sequences in finite populations
    • Tajima F. Evolutionary relationships of DNA sequences in finite populations. Genetics 1983, 105:437-460.
    • (1983) Genetics , vol.105 , pp. 437-460
    • Tajima, F.1
  • 38
    • 33749951044 scopus 로고
    • The out-group comparison method of character analysis
    • Watrous L.E., Wheeler Q.D. The out-group comparison method of character analysis. Syst. Zool. 1981, 30:1-11.
    • (1981) Syst. Zool. , vol.30 , pp. 1-11
    • Watrous, L.E.1    Wheeler, Q.D.2
  • 39
    • 84860577768 scopus 로고    scopus 로고
    • The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection
    • Yu Y., Degnan J.H., Nakhleh L. The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. PLoS One 2012, 8(4):e1002660.
    • (2012) PLoS One , vol.8 , Issue.4
    • Yu, Y.1    Degnan, J.H.2    Nakhleh, L.3


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