메뉴 건너뛰기




Volumn 856, Issue , 2012, Pages 239-272

Evolution of viral genomes: Interplay between selection, recombination, and other forces

Author keywords

Bayesian networks; Epistasis; Machine learning; Natural selection; Recombination; Viral evolution

Indexed keywords

ANIMAL; ARTICLE; GENETIC EPISTASIS; GENETIC RECOMBINATION; GENETIC SELECTION; GENETICS; GENOMICS; HUMAN; METHODOLOGY; MOLECULAR EVOLUTION; VIRUS GENOME;

EID: 84860181091     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-585-5_10     Document Type: Article
Times cited : (17)

References (60)
  • 2
    • 0031972161 scopus 로고    scopus 로고
    • Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    • Mar
    • R Nielsen and Z Yang. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics, 148(3):929-36, Mar 1998.
    • (1998) Genetics , vol.148 , Issue.3 , pp. 929-936
    • Nielsen, R.1    Yang, Z.2
  • 3
    • 49649108573 scopus 로고    scopus 로고
    • Comparative studies of RNA virus evolution
    • In Esteban Domingo, Colin Ross Parrish, and J J Holland, editors Elsevier, 2 edition
    • E C Holmes. Comparative studies of RNA virus evolution. In Esteban Domingo, Colin Ross Parrish, and J J Holland, editors, Origin and evolution of viruses, chapter 5, pages 119-134. Elsevier, 2 edition, 2008.
    • (2008) Origin and Evolution of Viruses Chapter 5 , pp. 119-134
    • Holmes, E.C.1
  • 6
    • 77954573744 scopus 로고    scopus 로고
    • Accurately measuring recombination between closely related HIV-1 genomes
    • Apr
    • Timothy E Schlub, Redmond P Smyth, Andrew J Grimm, Johnson Mak, and Miles P Davenport. Accurately measuring recombination between closely related HIV-1 genomes. PLoS Comput Biol, 6(4):e1000766, Apr 2010.
    • (2010) PLoS Comput. Biol. , vol.6 , Issue.4
    • Schlub, T.E.1    Smyth, R.P.2    Grimm, A.J.3    Johnson, M.4    Davenport, M.P.5
  • 9
    • 33645972304 scopus 로고    scopus 로고
    • A phylogenetic survey of recombination frequency in plant RNA viruses viruses
    • May
    • E R Chare and E C Holmes. A phylogenetic survey of recombination frequency in plant RNA viruses viruses. Arch Virol, 151 (5):933-46, May 2006.
    • (2006) Arch. Virol. , vol.151 , Issue.5 , pp. 933-946
    • Chare, E.R.1    Holmes, E.C.2
  • 10
    • 0142088791 scopus 로고    scopus 로고
    • Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses
    • Oct
    • Elizabeth R Chare, Ernest A Gould, and Edward C Holmes. Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses. J Gen Virol, 84(Pt 10):2691-703, Oct 2003.
    • (2003) J. Gen. Virol. , vol.84 , Issue.PT10 , pp. 2691-2703
    • Elizabeth, R.C.1    Ernest, A.G.2    Edward, C.H.3
  • 11
    • 0032853634 scopus 로고    scopus 로고
    • Evolutionary aspects of recombination in RNA viruses
    • Oct
    • M Worobey and E C Holmes. Evolutionary aspects of recombination in RNA viruses. J Gen Virol, 80 (Pt 10):2535-43, Oct 1999.
    • (1999) J. Gen. Virol. , vol.80 , Issue.PT10 , pp. 2535-2543
    • Worobey, M.1    Holmes, E.C.2
  • 13
    • 0035923699 scopus 로고    scopus 로고
    • Evaluation of methods for detecting recombination from DNA sequences: Computer simulations
    • Nov
    • D Posada and K A Crandall. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci USA, 98(24): 13757-62, Nov 2001.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , Issue.24 , pp. 13757-62
    • Posada, D.1    Crandall, K.A.2
  • 15
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Jul.
    • N Saitou and M Nei. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol, 4(4):406-25, Jul 1987.
    • (1987) Mol. Biol. Evol. , vol.4 , Issue.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 16
    • 0027157960 scopus 로고
    • Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
    • May
    • K Tamura and M Nei. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol, 10(3):512-26, May 1993.
    • (1993) Mol. Biol. Evol. , vol.10 , Issue.3 , pp. 512-526
    • Tamura, K.1    Nei, M.2
  • 17
    • 68049135942 scopus 로고    scopus 로고
    • Detecting signatures of selection from DNA sequences using datamonkey
    • Art F Y Poon, Simon D W Frost, and Sergei L Kosakovsky Pond. Detecting signatures of selection from DNA sequences using datamonkey. Methods Mol Biol, 537:163-83, 2009.
    • (2009) Methods Mol. Biol. , vol.537 , pp. 163-183
    • Art, F.Y.P.1    Simon, D.W.F.2    Sergei, L.K.P.3
  • 18
    • 0032766857 scopus 로고    scopus 로고
    • Multiple comparisons of log-likelihoods with applications to phylogenetic inference
    • H. Shimodaira and M. Hasegawa. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol, 16:1114-1116, 1999.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1114-1116
    • Shimodaira, H.1    Hasegawa, M.2
  • 19
    • 0034351387 scopus 로고    scopus 로고
    • Likelihood-based tests of topologies in phylogenetics
    • Dec
    • N Goldman, J P Anderson, and A G Rodrigo. Likelihood-based tests of topologies in phylogenetics. Syst Biol, 49(4):652-70, Dec 2000.
    • (2000) Syst. Biol. , vol.49 , Issue.4 , pp. 652-670
    • Goldman, N.1    Anderson, J.P.2    Rodrigo, A.G.3
  • 22
    • 0024579619 scopus 로고
    • Resistance to antiviral drugs: The end of innocence
    • Feb
    • M S Hirsch and R T Schooley. Resistance to antiviral drugs: The end of innocence. N Engl J Med, 320(5):313-4, Feb 1989.
    • (1989) N. Engl. J. Med. , vol.320 , Issue.5 , pp. 313-314
    • Hirsch, M.S.1    Schooley, R.T.2
  • 23
    • 0042208362 scopus 로고    scopus 로고
    • Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites
    • Jul
    • Maria Anisimova, Rasmus Nielsen, and Ziheng Yang. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics, 164(3): 1229-36, Jul 2003.
    • (2003) Genetics , vol.164 , Issue.3 , pp. 1229-1236
    • Maria, A.1    Rasmus, N.2    Ziheng, Y.3
  • 24
    • 33749827106 scopus 로고    scopus 로고
    • Robust inference of positive selection from recombining coding sequences
    • Oct
    • Konrad Scheffler, Darren P Martin, and Cathal Seoighe. Robust inference of positive selection from recombining coding sequences. Bioinformatics, 2(20):2493-9, Oct 2006.
    • (2006) Bioinformatics , vol.2 , Issue.20 , pp. 2493-2499
    • Konrad, S.1    Darren, P.M.2    Cathal, S.3
  • 25
    • 60849132764 scopus 로고    scopus 로고
    • Models of coding sequence evolution
    • January
    • Wayne Delport, Konrad Scheffler, and Cathal Seoighe. Models of coding sequence evolution. Briefings in bioinformatics, 10(1):97-109, January 2009.
    • (2009) Briefings in Bioinformatics , vol.10 , Issue.1 , pp. 97-109
    • Wayne, D.1    Konrad, S.2    Cathal, S.3
  • 26
    • 27844569825 scopus 로고    scopus 로고
    • Site-to-site variation of synonymous substitution rates
    • Dec
    • Sergei Kosakovsky Pond and Spencer V Muse. Site-to-site variation of synonymous substitution rates. Mol Biol Evol, 22(12):2375-85, Dec 2005.
    • (2005) Mol. Biol. Evol. , vol.22 , Issue.12 , pp. 2375-2385
    • Sergei, K.P.1    Spencer, V.M.2
  • 28
    • 34748817463 scopus 로고    scopus 로고
    • Looking for darwin in all the wrong places: The misguided quest for positive selection at the nucleotide sequence level
    • July
    • A. L. Hughes. Looking for darwin in all the wrong places: The misguided quest for positive selection at the nucleotide sequence level. Heredity, 99(4):364-373, July 2007.
    • (2007) Heredity , vol.99 , Issue.4 , pp. 364-373
    • Hughes, A.L.1
  • 31
    • 0000625869 scopus 로고
    • Rice. Analyzing tables of statistical tests
    • William R. Rice. Analyzing tables of statistical tests. Evolution, 43(1):223-225, 1989.
    • (1989) Evolution , vol.43 , Issue.1 , pp. 223-225
    • William, R.1
  • 32
    • 84860195874 scopus 로고    scopus 로고
    • Modeling HIV-1 drug resistance as episodic directional selection
    • revision
    • Ben Murrell, Tulio de Oliviera, Chris Seebregts, Sergei L Kosakovsky Pond, and Konrad Scheffler. Modeling HIV-1 drug resistance as episodic directional selection. Mol Biol Evol, in revision, 2011.
    • (2011) Mol. Biol. Evol.
    • Ben, M.1    De Oliviera, T.2    Chris, S.3    Sergei, L.K.P.4    Konrad, S.5
  • 33
    • 49749094696 scopus 로고    scopus 로고
    • A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza a virus
    • September 2008
    • Sergei L. Kosakovsky Pond, Art F. Y. Poon, Andrew J. Leigh Brown, and Simon D. W Frost. A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza a virus. Mol Biol Evol, 25(9): 1809-1824, September 2008.
    • Mol. Biol. Evol. , vol.25 , Issue.9 , pp. 1809-1824
    • Sergei, L.K.P.1    Art, F.Y.P.2    Andrew, J.3    Leigh, B.4    Simon, D.W.F.5
  • 35
    • 0035198377 scopus 로고    scopus 로고
    • Modeling genetic architecture: A multilinear theory of gene interaction
    • Feb
    • T F Hansen and G PWagner. Modeling genetic architecture: A multilinear theory of gene interaction. Theor Popul Biol, 59(1):61-86, Feb 2001.
    • (2001) Theor. Popul. Biol. , vol.59 , Issue.1 , pp. 61-86
    • Hansen, T.F.1    Wagner, G.P.2
  • 37
    • 36948998606 scopus 로고    scopus 로고
    • An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope
    • Nov
    • Art F Y Poon, Fraser I Lewis, Sergei L Kosakovsky Pond, and Simon D W Frost. An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope. PLoS Comput Biol, 3(11):e231, Nov 2007.
    • (2007) PLoS Comput. Biol. , vol.3 , Issue.11
    • Art, F.Y.P.1    Fraser, I.L.2    Sergei, L.K.P.3    Simon, D.W.F.4
  • 38
    • 38049186804 scopus 로고    scopus 로고
    • Correlated substitution analysis and the prediction of amino acid structural contacts
    • Jan
    • David S Horner, Walter PiroVano, and Graziano Pesole. Correlated substitution analysis and the prediction of amino acid structural contacts. Brief Bioinform, 9(1):46-56, Jan 2008.
    • (2008) Brief Bioinform. , vol.9 , Issue.1 , pp. 46-56
    • David, S.H.1    Walter, P.V.2    Graziano, P.3
  • 39
    • 85072724479 scopus 로고    scopus 로고
    • Why should we care about molecular coevolution
    • Francisco M Codoñer and Mario A Fares. Why should we care about molecular coevolution? Evol Bioinform Online, 4:29-38, 2008.
    • (2008) Evol. Bioinform. Online , vol.4 , pp. 29-38
    • Francisco, M.C.1    Mario, A.F.2
  • 40
    • 77956219920 scopus 로고    scopus 로고
    • Validation of coevolving residue algorithms via pipeline sensitivity analysis: ELSC and OMES and ZNMI
    • Christopher A Brown and Kevin S Brown. Validation of coevolving residue algorithms via pipeline sensitivity analysis: ELSC and OMES and ZNMI, oh my! PLoS One, 5(6):e10779, 2010.
    • (2010) Oh My! PLoS One , vol.5 , Issue.6
    • Christopher, A.B.1    Kevin, S.B.2
  • 41
    • 0028295169 scopus 로고
    • Correlated mutations and residue contacts in proteins
    • Apr
    • U Göbel, C Sander, R Schneider, and A Valencia. Correlated mutations and residue contacts in proteins. Proteins, 18(4):309-17, Apr 1994.
    • (1994) Proteins , vol.18 , Issue.4 , pp. 309-317
    • Göbel, U.1    Sander, C.2    Schneider, R.3    Valencia, A.4
  • 42
    • 0027297096 scopus 로고
    • Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: An information theoretic analysis
    • Aug
    • B T Korber, RMFarber, DHWolpert, and A S Lapedes. Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: An information theoretic analysis. Proc Natl Acad Sci U S A, 90 (15):7176-80, Aug 1993.
    • (1993) Proc. Natl. Acad. Sci. U S A , vol.90 , Issue.15 , pp. 7176-7180
    • Korber, B.T.1    Farber, R.M.2    Wolpert, D.H.3    Lapedes, A.S.4
  • 43
    • 0022203256 scopus 로고
    • Phylogenies and the comparative method
    • J. Felsenstein. Phylogenies and the comparative method. Am. Nat., 125(1): 1-15, 1985.
    • (1985) Am. Nat. , vol.125 , Issue.1 , pp. 1-15
    • Felsenstein, J.1
  • 44
    • 50549084385 scopus 로고    scopus 로고
    • Spidermonkey: Rapid detection of co-evolving sites using bayesian graphical models
    • Sep
    • Art F Y Poon, Fraser I Lewis, Simon D W Frost, and Sergei L Kosakovsky Pond. Spidermonkey: rapid detection of co-evolving sites using bayesian graphical models. Bioinformatics, 24(17): 1949-50, Sep 2008.
    • (2008) Bioinformatics , vol.24 , Issue.17 , pp. 1949-1950
    • Art, F.Y.P.1    Fraser, I.L.2    Simon, D.W.F.3    Sergei, L.K.P.4
  • 45
    • 0034117082 scopus 로고    scopus 로고
    • A fast algorithm for joint reconstruction of ancestral amino acid sequences
    • Jun
    • T Pupko, I Pe'er, R Shamir, and DGraur. A fast algorithm for joint reconstruction of ancestral amino acid sequences. Mol Biol Evol, 17(6): 890-6, Jun 2000.
    • (2000) Mol. Biol. Evol. , vol.17 , Issue.6 , pp. 890-896
    • Pupko, T.1    Peer, I.2    Shamir, R.3    Graur, D.4
  • 46
    • 0033744204 scopus 로고    scopus 로고
    • Exploring a phylogenetic approach for the detection of correlated substitutions in proteins
    • Nov
    • P Tuff and P Darlu. Exploring a phylogenetic approach for the detection of correlated substitutions in proteins. Mol Biol Evol, 17(11): 1753-9, Nov 2000.
    • (2000) Mol. Biol. Evol. , vol.17 , Issue.11 , pp. 1753-1759
    • Tuff, P.1    Darlu, P.2
  • 47
    • 0036804625 scopus 로고    scopus 로고
    • Mapping mutations on phylogenies
    • Oct
    • Rasmus Nielsen. Mapping mutations on phylogenies. Syst Biol, 51(5):729-39, Oct 2002.
    • (2002) Syst. Biol. , vol.51 , Issue.5 , pp. 729-739
    • Rasmus, N.1
  • 48
    • 23944476399 scopus 로고    scopus 로고
    • A model-based approach for detecting coevolving positions in a molecule
    • Sep
    • Julien Dutheil, Tal Pupko, Alain Jean-Marie, and Nicolas Galtier. A model-based approach for detecting coevolving positions in a molecule. Mol Biol Evol, 22(9): 1919-28, Sep 2005.
    • (2005) Mol. Biol. Evol. , vol.22 , Issue.9 , pp. 1919-1928
    • Julien, D.1    Tal, P.2    Alain, J.-M.3    Nicolas, G.4
  • 49
    • 33748170576 scopus 로고    scopus 로고
    • A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution
    • Sep
    • Beth Shapiro, Andrew Rambaut, Oliver G Pybus, and Edward C Holmes. A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution. Mol Biol Evol, 23(9): 1724-30, Sep 2006.
    • (2006) Mol. Biol. Evol. , vol.23 , Issue.9 , pp. 1724-1730
    • Shapir, B.1    Rambaut, A.2    Pybus, O.G.3    Holmes, E.C.4
  • 50
    • 0038521713 scopus 로고    scopus 로고
    • Stochastic mapping of morphological characters
    • Apr
    • John P Huelsenbeck, Rasmus Nielsen, and Jonathan P Bollback. Stochastic mapping of morphological characters. Syst Biol, 52(2): 131-58, Apr 2003.
    • (2003) Syst. Biol. , vol.52 , Issue.2 , pp. 131-158
    • John, P.H.1    Rasmus, N.2    Jonathan, P.B.3
  • 52
    • 0037262841 scopus 로고    scopus 로고
    • Being bayesian about network structure a bayesian approach to structure discovery in Bayesian networks
    • 10.1023/A 020249912095
    • Nir Friedman and Daphne Koller. Being bayesian about network structure. a bayesian approach to structure discovery in Bayesian networks. Machine Learning, 50:95-125, 2003. 10.1023/A: 1020249912095.
    • (2003) Machine Learning , vol.50 , Issue.95-125
    • Nir, F.1    Daphne, K.2
  • 54
    • 77956890234 scopus 로고
    • Monte Carlo sampling methods using Markov chains and their applications
    • W. K. Hastings. Monte Carlo sampling methods using Markov chains and their applications. Biometrika, 57(1):97-109, 1970.
    • (1970) Biometrika , vol.57 , Issue.1 , pp. 97-109
    • Hastings, W.K.1
  • 55
    • 0025629621 scopus 로고
    • The causes of natural selection
    • M J Wade and S Kalisz. The causes of natural selection. Evolution, 44(8): 1947-1955, 1990.
    • (1990) Evolution , vol.44 , Issue.8 , pp. 1947-1955
    • Wade, M.J.1    Kalisz, S.2
  • 57
    • 37049038445 scopus 로고    scopus 로고
    • Mapping protease inhibitor resistance to human immunodeficiency virus type 1 sequence polymorphisms within patients
    • Dec
    • Art F Y Poon, Sergei L Kosakovsky Pond, Douglas D Richman, and Simon D W Frost. Mapping protease inhibitor resistance to human immunodeficiency virus type 1 sequence polymorphisms within patients. J Virol, 81(24):13598-607, Dec 2007.
    • (2007) J. Virol. , vol.81 , Issue.24 , pp. 13598-607
    • Art, F.Y.P.1    Sergei, L.K.P.2    Douglas, D.R.3    Simon, D.W.F.4
  • 58
    • 0036784572 scopus 로고    scopus 로고
    • Magnitude and frequency of cytotoxic T-lymphocyte responses: Identification of immunodominant regions of human immunodeficiency virus type 1 subtype C
    • Oct
    • V Novitsky, H Cao, N Rybak, P Gilbert, M F McLane, S Gaolekwe, T Peter, I Thior, T Ndung'u, R Marlink, T H Lee, and M Essex. Magnitude and frequency of cytotoxic T-lymphocyte responses: identification of immunodominant regions of human immunodeficiency virus type 1 subtype C. J Virol, 76(20): 10155-68, Oct 2002.
    • (2002) J. Virol. , vol.76 , Issue.20 , pp. 10155-68
    • Novitsky, V.1    Cao, H.2    Rybak, N.3    Gilbert, P.4    McLane, M.F.5    Gaolekwe, S.6    Peter, T.7    Thior, I.8    Ndung'U, T.9    Marlink, R.10    Lee, T.H.11    Essex, M.12
  • 59
    • 0030906043 scopus 로고    scopus 로고
    • Recognition of a small number of diverse epitopes dominates the cytotoxic T lymphocytes response to HIV type 1 in an infected individual
    • Mar
    • J Lieberman, J A Fabry, D M Fong, and G R Parkerson, 3rd. Recognition of a small number of diverse epitopes dominates the cytotoxic T lymphocytes response to HIV type 1 in an infected individual. AIDS Res Hum Retroviruses, 13(5):383-92, Mar 1997.
    • (1997) AIDS Res. Hum. Retroviruses , vol.13 , Issue.5 , pp. 383-392
    • Lieberman, J.1    Fabry, J.A.2    Fong, D.M.3    Iii Parkerson, G.R.4
  • 60
    • 17744396121 scopus 로고    scopus 로고
    • Not so different after all: A comparison of methods for detecting amino acid sites under selection
    • May
    • Sergei L. Kosakovsky Pond and Simon D. W. Frost. Not so different after all: A comparison of methods for detecting amino acid sites under selection. Mol Biol Evol, 22(5): 1208-1222, May 2005.
    • (2005) Mol. Biol. Evol. , vol.22 , Issue.5 , pp. 1208-1222
    • Sergei, L.1    Kosakovsky, P.2    Simon, D.W.F.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.