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Volumn 110, Issue 46, 2013, Pages 18566-18571

Topology of viral evolution

Author keywords

Gene flow; Persistent homology; Topological data analysis

Indexed keywords

ARTICLE; AVIAN INFLUENZA VIRUS; CLONAL EVOLUTION; EVOLUTION; GENETIC REASSORTMENT; HUMAN IMMUNODEFICIENCY VIRUS 1; INFLUENZA VIRUS A H7N9; MOLECULAR PHYLOGENY; NONHUMAN; PRIORITY JOURNAL; RNA VIRUS; VIRAL EVOLUTION; VIRAL GENETICS; VIRUS MORPHOLOGY; VIRUS RECOMBINATION;

EID: 84887457901     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1313480110     Document Type: Article
Times cited : (271)

References (44)
  • 2
    • 0036021407 scopus 로고    scopus 로고
    • Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data
    • Drummond AJ, Nicholls GK, Rodrigo AG, Solomon W (2002) Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161(3):1307-1320. (Pubitemid 34831453)
    • (2002) Genetics , vol.161 , Issue.3 , pp. 1307-1320
    • Drummond, A.J.1    Nicholls, G.K.2    Rodrigo, A.G.3    Solomon, W.4
  • 3
    • 0022436876 scopus 로고
    • Stochastic errors in DNA evolution and molecular phylogeny
    • Nei M (1986) Stochastic errors in DNA evolution and molecular phylogeny. Prog Clin Biol Res 218:133-147.
    • (1986) Prog Clin Biol Res , vol.218 , pp. 133-147
    • Nei, M.1
  • 4
    • 0033603539 scopus 로고    scopus 로고
    • Phylogenetic classification and the universal tree
    • Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284(5423): 2124-2129.
    • (1999) Science , vol.284 , Issue.5423 , pp. 2124-2129
    • Doolittle, W.F.1
  • 5
    • 0036948655 scopus 로고    scopus 로고
    • Recombination in evolutionary genomics
    • DOI 10.1146/annurev.genet.36.040202.111115
    • Posada D, Crandall KA, Holmes EC (2002) Recombination in evolutionary genomics. Annu Rev Genet 36:75-97. (Pubitemid 36109184)
    • (2002) Annual Review of Genetics , vol.36 , pp. 75-97
    • Posada, D.1    Crandall, K.A.2    Holmes, E.C.3
  • 6
    • 13144283628 scopus 로고    scopus 로고
    • A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints
    • DOI 10.1089/aid.2005.21.98
    • Martin DP, Posada D, Crandall KA, Williamson C (2005) A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res Hum Retroviruses 21(1):98-102. (Pubitemid 40179806)
    • (2005) AIDS Research and Human Retroviruses , vol.21 , Issue.1 , pp. 98-102
    • Martin, D.P.1    Posada, D.2    Crandall, K.A.3    Williamson, C.4
  • 7
    • 0034097468 scopus 로고    scopus 로고
    • TOPAL 2.0: Improved detection of mosaic sequences within multiple alignments
    • McGuire G, Wright F (2000) TOPAL 2.0: improved detection of mosaic sequences within multiple alignments. Bioinformatics 16(2):130-134. (Pubitemid 30248589)
    • (2000) Bioinformatics , vol.16 , Issue.2 , pp. 130-134
    • McGuire, G.1    Wright, F.2
  • 8
    • 21444455535 scopus 로고    scopus 로고
    • Dual multiple change-point model leads to more accurate recombination detection
    • DOI 10.1093/bioinformatics/bti459
    • Minin VN, Dorman KS, Fang F, Suchard MA (2005) Dual multiple change-point model leads to more accurate recombination detection. Bioinformatics 21(13):3034-3042. (Pubitemid 40916429)
    • (2005) Bioinformatics , vol.21 , Issue.13 , pp. 3034-3042
    • Minin, V.N.1    Dorman, K.S.2    Fang, F.3    Suchard, M.A.4
  • 10
    • 0031897789 scopus 로고    scopus 로고
    • Detecting recombination from gene trees
    • Maynard Smith J, Smith NH (1998) Detecting recombination from gene trees. Mol Biol Evol 15(5):590-599.
    • (1998) Mol Biol Evol , vol.15 , Issue.5 , pp. 590-599
    • Maynard Smith, J.1    Smith, N.H.2
  • 11
    • 33646167864 scopus 로고    scopus 로고
    • A simple and robust statistical test for detecting the presence of recombination
    • Bruen TC, Philippe H, Bryant D (2006) A simple and robust statistical test for detecting the presence of recombination. Genetics 172(4):2665-2681.
    • (2006) Genetics , vol.172 , Issue.4 , pp. 2665-2681
    • Bruen, T.C.1    Philippe, H.2    Bryant, D.3
  • 12
    • 0029963710 scopus 로고    scopus 로고
    • A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences
    • Jakobsen IB, Easteal S (1996) A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences. Comput Appl Biosci 12(4):291-295. (Pubitemid 26345164)
    • (1996) Computer Applications in the Biosciences , vol.12 , Issue.4 , pp. 291-295
    • Jakobsen, I.B.1    Easteal, S.2
  • 13
    • 0026708873 scopus 로고
    • Analyzing the mosaic structure of genes
    • Smith JM (1992) Analyzing the mosaic structure of genes. J Mol Evol 34(2):126-129.
    • (1992) J Mol Evol , vol.34 , Issue.2 , pp. 126-129
    • Smith, J.M.1
  • 14
    • 0031026942 scopus 로고    scopus 로고
    • Networks and viral evolution
    • Fitch WM (1997) Networks and viral evolution. J Mol Evol 44(Suppl 1):S65-S75.
    • (1997) J Mol Evol , vol.44 , Issue.SUPPL. 1
    • Fitch, W.M.1
  • 15
    • 3042637206 scopus 로고    scopus 로고
    • Using consensus networks to visualize contradictory evidence for species phylogeny
    • DOI 10.1093/molbev/msh145
    • Holland BR, Huber KT, Moulton V, Lockhart PJ (2004) Using consensus networks to visualize contradictory evidence for species phylogeny. Mol Biol Evol 21(7):1459-1461. (Pubitemid 38823749)
    • (2004) Molecular Biology and Evolution , vol.21 , Issue.7 , pp. 1459-1461
    • Holland, B.R.1    Huber, K.T.2    Moulton, V.3    Lockhart, P.J.4
  • 16
    • 30744470609 scopus 로고    scopus 로고
    • Application of phylogenetic networks in evolutionary studies
    • DOI 10.1093/molbev/msj030
    • Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23(2):254-267. (Pubitemid 43100040)
    • (2006) Molecular Biology and Evolution , vol.23 , Issue.2 , pp. 254-267
    • Huson, D.H.1    Bryant, D.2
  • 18
    • 45049086039 scopus 로고    scopus 로고
    • Seeing the trees and their branches in the network is hard
    • Kanj IA, Nakhleh L, Than C, Xia G (2008) Seeing the trees and their branches in the network is hard. Theor Comput Sci 401(1-3):153-164.
    • (2008) Theor Comput Sci , vol.401 , Issue.1-3 , pp. 153-164
    • Kanj, I.A.1    Nakhleh, L.2    Than, C.3    Xia, G.4
  • 19
    • 77954178859 scopus 로고    scopus 로고
    • Phylogenetic networks do not need to be complex: Using fewer reticulations to represent conflicting clusters
    • van Iersel L, Kelk S, Rupp R, Huson D (2010) Phylogenetic networks do not need to be complex: Using fewer reticulations to represent conflicting clusters. Bioinformatics 26(12):i124-i131.
    • (2010) Bioinformatics , vol.26 , Issue.12
    • Van Iersel, L.1    Kelk, S.2    Rupp, R.3    Huson, D.4
  • 20
    • 77957862332 scopus 로고    scopus 로고
    • Phylogenetic networks: Concepts, algorithms and applications
    • Kelk S (2011) Phylogenetic networks: Concepts, algorithms and applications. Syst Biol 61(1):174-175.
    • (2011) Syst Biol , vol.61 , Issue.1 , pp. 174-175
    • Kelk, S.1
  • 21
    • 3242876395 scopus 로고    scopus 로고
    • Optimal, efficient reconstruction of phylogenetic networks with constrained recombination
    • DOI 10.1142/S0219720004000521
    • Gusfield D, Eddhu S, Langley C (2004) Optimal, efficient reconstruction of phylogenetic networks with constrained recombination. J Bioinform Comput Biol 2(1):173-213. (Pubitemid 38996817)
    • (2004) Journal of Bioinformatics and Computational Biology , vol.2 , Issue.1 , pp. 173-213
    • Gusfield, D.1    Eddhu, S.2    Langley, C.3
  • 25
    • 0023612034 scopus 로고
    • Estimating the recombination parameter of a finite population model without selection
    • Hudson RR (1987) Estimating the recombination parameter of a finite population model without selection. Genet Res 50(3):245-250.
    • (1987) Genet Res , vol.50 , Issue.3 , pp. 245-250
    • Hudson, R.R.1
  • 26
    • 0036199914 scopus 로고    scopus 로고
    • A coalescent-based method for detecting and estimating recombination from gene sequences
    • McVean G, Awadalla P, Fearnhead P (2002) A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160(3):1231-1241. (Pubitemid 34263482)
    • (2002) Genetics , vol.160 , Issue.3 , pp. 1231-1241
    • McVean, G.1    Awadalla, P.2    Fearnhead, P.3
  • 28
    • 77952111176 scopus 로고    scopus 로고
    • Characteristic features of InfA-15 monoclonal antibody recognizing H1, H3, and H5 subtypes of hemagglutinin of influenza virus A type
    • Hifumi E, Fujimoto N, Ishida K, Kawawaki H, Uda T (2010) Characteristic features of InfA-15 monoclonal antibody recognizing H1, H3, and H5 subtypes of hemagglutinin of influenza virus A type. J Biosci Bioeng 109(6):598-608.
    • (2010) J Biosci Bioeng , vol.109 , Issue.6 , pp. 598-608
    • Hifumi, E.1    Fujimoto, N.2    Ishida, K.3    Kawawaki, H.4    Uda, T.5
  • 29
    • 84867518731 scopus 로고    scopus 로고
    • Estimating reassortment rates in co-circulating Eurasian swine influenza viruses
    • Combating Swine Influenza Initiative-COSI Consortium
    • Lycett SJ, et al.; Combating Swine Influenza Initiative-COSI Consortium (2012) Estimating reassortment rates in co-circulating Eurasian swine influenza viruses. J Gen Virol 93(Pt 11):2326-2336.
    • (2012) J Gen Virol , vol.93 , Issue.PART 11 , pp. 2326-2336
    • Lycett, S.J.1
  • 30
    • 24944468625 scopus 로고    scopus 로고
    • Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses
    • Holmes EC, et al. (2005) Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol 3(9):e300.
    • (2005) PLoS Biol , vol.3 , Issue.9
    • Holmes, E.C.1
  • 31
    • 0018412958 scopus 로고
    • Nonrandom association of parental genes in influenza A virus recombinants
    • DOI 10.1016/0042-6822(79)90430-6
    • Lubeck MD, Palese P, Schulman JL (1979) Nonrandom association of parental genes in influenza A virus recombinants. Virology 95(1):269-274. (Pubitemid 9171808)
    • (1979) Virology , vol.95 , Issue.1 , pp. 269-274
    • Lubeck, M.D.1    Palese, P.2    Schulman, J.L.3
  • 32
    • 44949193800 scopus 로고    scopus 로고
    • The evolutionary genetics and emergence of avian influenza viruses in wild birds
    • Dugan VG, et al. (2008) The evolutionary genetics and emergence of avian influenza viruses in wild birds. PLoS Pathog 4(5):e1000076.
    • (2008) PLoS Pathog , vol.4 , Issue.5
    • Dugan, V.G.1
  • 33
    • 84887478649 scopus 로고    scopus 로고
    • The world waits for H7N9 to yield up its secrets
    • Holmes D (2013) The world waits for H7N9 to yield up its secrets. Lancet Infect Dis 13(6):477-478.
    • (2013) Lancet Infect Dis , vol.13 , Issue.6 , pp. 477-478
    • Holmes, D.1
  • 34
    • 84877785371 scopus 로고    scopus 로고
    • Human infection with a novel avian-origin influenza A (H7N9) virus
    • Gao R, et al. (2013) Human infection with a novel avian-origin influenza A (H7N9) virus. N Engl J Med 368(20):1888-1897.
    • (2013) N Engl J Med , vol.368 , Issue.20 , pp. 1888-1897
    • Gao, R.1
  • 35
    • 34447249033 scopus 로고    scopus 로고
    • Contribution of recombination to the evolution of human immunodeficiency viruses expressing resistance to antiretroviral treatment
    • DOI 10.1128/JVI.00083-07
    • Nora T, et al. (2007) Contribution of recombination to the evolution of human immunodeficiency viruses expressing resistance to antiretroviral treatment. J Virol 81(14):7620-7628. (Pubitemid 47047847)
    • (2007) Journal of Virology , vol.81 , Issue.14 , pp. 7620-7628
    • Nora, T.1    Charpentier, C.2    Tenaillon, O.3    Hoede, C.4    Clavel, F.5    Hance, A.J.6
  • 42
    • 70350344982 scopus 로고    scopus 로고
    • Recombination in West Nile Virus: Minimal contribution to genomic diversity
    • Pickett BE, Lefkowitz EJ (2009) Recombination in West Nile Virus: Minimal contribution to genomic diversity. Virol J 6(1):165-171.
    • (2009) Virol J , vol.6 , Issue.1 , pp. 165-171
    • Pickett, B.E.1    Lefkowitz, E.J.2
  • 43
    • 1542676372 scopus 로고    scopus 로고
    • Microevolution and virulence of dengue viruses
    • Rico-Hesse R (2003) Microevolution and virulence of dengue viruses. Adv Virus Res 59:315-341.
    • (2003) Adv Virus Res , vol.59 , pp. 315-341
    • Rico-Hesse, R.1
  • 44
    • 0142088791 scopus 로고    scopus 로고
    • Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses
    • DOI 10.1099/vir.0.19277-0
    • Chare ER, Gould EA, Holmes EC (2003) Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses. J Gen Virol 84(Pt 10):2691-2703. (Pubitemid 37321311)
    • (2003) Journal of General Virology , vol.84 , Issue.10 , pp. 2691-2703
    • Chare, E.R.1    Gould, E.A.2    Holmes, E.C.3


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