메뉴 건너뛰기




Volumn 6, Issue , 2016, Pages

Germline viral "fossils" guide in silico reconstruction of a mid-Cenozoic era marsupial adeno-associated virus

Author keywords

[No Author keywords available]

Indexed keywords

ADENO ASSOCIATED VIRUS; FAUNA; FOSSIL; GENOME; GERM LINE; PHYLOGENY; RUPELIAN; SCREENING; SPECIES DIFFERENTIATION; TRANSLATIONAL RESEARCH; UPPER EOCENE; VIRUS CAPSID; WALLABY; ANIMAL; BIOLOGY; CLASSIFICATION; DEPENDOPARVOVIRUS; GENETICS; GERM CELL; MARSUPIAL; MOLECULAR EVOLUTION; VIROLOGY;

EID: 84977275461     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep28965     Document Type: Article
Times cited : (30)

References (95)
  • 1
    • 78649718268 scopus 로고    scopus 로고
    • Endogenous viral elements in animal genomes
    • Katzourakis, A. & Gifford, R. J. Endogenous viral elements in animal genomes. PLos Genet 6, e1001191 (2010).
    • (2010) PLos Genet , vol.6
    • Katzourakis, A.1    Gifford, R.J.2
  • 2
    • 77957921403 scopus 로고    scopus 로고
    • Genomic fossils calibrate the long-term evolution of hepadnaviruses
    • Gilbert, C. & Feschotte, C. Genomic fossils calibrate the long-term evolution of hepadnaviruses. PLos Biol 8, e1000495 (2010).
    • (2010) PLos Biol , vol.8
    • Gilbert, C.1    Feschotte, C.2
  • 3
    • 78049503885 scopus 로고    scopus 로고
    • Sequences from ancestral single-stranded DNA viruses in vertebrate genomes: The parvoviridae and circoviridae are more than 40 to 50 million years old
    • Belyi, V. A., Levine, A. J. & Skalka, A. M. Sequences from ancestral single-stranded DNA viruses in vertebrate genomes: the parvoviridae and circoviridae are more than 40 to 50 million years old. J Virol 84, 12458-12462 (2010).
    • (2010) J Virol , vol.84 , pp. 12458-12462
    • Belyi, V.A.1    Levine, A.J.2    Skalka, A.M.3
  • 4
    • 77957660360 scopus 로고    scopus 로고
    • Unexpected inheritance: Multiple integrations of ancient bornavirus and ebolavirus/ marburgvirus sequences in vertebrate genomes
    • Belyi, V. A., Levine, A. J. & Skalka, A. M. Unexpected inheritance: multiple integrations of ancient bornavirus and ebolavirus/ marburgvirus sequences in vertebrate genomes. PLos Pathog 6, e1001030 (2010).
    • (2010) PLos Pathog , vol.6
    • Belyi, V.A.1    Levine, A.J.2    Skalka, A.M.3
  • 5
    • 79960944025 scopus 로고    scopus 로고
    • Widespread endogenization of genome sequences of non-retroviral RNA viruses into plant genomes
    • Chiba, S. et al. Widespread endogenization of genome sequences of non-retroviral RNA viruses into plant genomes. PLos Pathog 7, e1002146 (2011).
    • (2011) PLos Pathog , vol.7
    • Chiba, S.1
  • 6
    • 80053342292 scopus 로고    scopus 로고
    • Widespread endogenization of densoviruses and parvoviruses in animal and human genomes
    • Liu, H. et al. Widespread endogenization of densoviruses and parvoviruses in animal and human genomes. J Virol 85, 9863-9876 (2011).
    • (2011) J Virol , vol.85 , pp. 9863-9876
    • Liu, H.1
  • 7
    • 84999570886 scopus 로고    scopus 로고
    • Endogenous hepadnaviruses, bornaviruses and circoviruses in snakes
    • Gilbert, C. et al. Endogenous hepadnaviruses, bornaviruses and circoviruses in snakes. Proc Biol Sci 281, 20141122 (2014).
    • (2014) Proc Biol Sci , vol.281
    • Gilbert, C.1
  • 8
    • 84899970268 scopus 로고    scopus 로고
    • The family Parvoviridae
    • Cotmore, S. F. et al. The family Parvoviridae. Arch Virol 159, 1239-1247 (2014).
    • (2014) Arch Virol , vol.159 , pp. 1239-1247
    • Cotmore, S.F.1
  • 9
    • 78649438177 scopus 로고    scopus 로고
    • Discovery and characterization of mammalian endogenous parvoviruses
    • Kapoor, A., Simmonds, P. & Lipkin, W. I. Discovery and characterization of mammalian endogenous parvoviruses. J Virol 84, 12628-12635 (2010).
    • (2010) J Virol , vol.84 , pp. 12628-12635
    • Kapoor, A.1    Simmonds, P.2    Lipkin, W.I.3
  • 10
    • 0014143050 scopus 로고
    • Isolation of adenovirus-associated viruses from man
    • Blacklow, N. R., Hoggan, M. D. & Rowe, W. P. Isolation of adenovirus-associated viruses from man. Proc Natl Acad Sci USA 58, 1410-1415 (1967).
    • (1967) Proc Natl Acad Sci USA , vol.58 , pp. 1410-1415
    • Blacklow, N.R.1    Hoggan, M.D.2    Rowe, W.P.3
  • 11
    • 0016987513 scopus 로고
    • Isolation and characterization of adeno-associated viruses from bovine adenovirus types 1 and 2
    • Myrup, A. C., Mohanty, S. B. & Hetrick, F. M. Isolation and characterization of adeno-associated viruses from bovine adenovirus types 1 and 2. Am J Vet Res 37, 907-910 (1976).
    • (1976) Am J Vet Res , vol.37 , pp. 907-910
    • Myrup, A.C.1    Mohanty, S.B.2    Hetrick, F.M.3
  • 12
    • 0037015049 scopus 로고    scopus 로고
    • Novel adeno-associated viruses from rhesus monkeys as vectors for human gene therapy
    • Gao, G. P. et al. Novel adeno-associated viruses from rhesus monkeys as vectors for human gene therapy. Proc Natl Acad Sci USA 99, 11854-11859 (2002).
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 11854-11859
    • Gao, G.P.1
  • 13
    • 2642512201 scopus 로고    scopus 로고
    • Clades of adeno-associated viruses are widely disseminated in human tissues
    • Gao, G. et al. Clades of adeno-associated viruses are widely disseminated in human tissues. J Virol 78, 6381-6388 (2004).
    • (2004) J Virol , vol.78 , pp. 6381-6388
    • Gao, G.1
  • 14
    • 29744466489 scopus 로고    scopus 로고
    • Novel caprine adeno-associated virus (AAV) capsid (AAV-Go.1) is closely related to the primate AAV-5 and has unique tropism and neutralization properties
    • Arbetman, A. E. et al. Novel caprine adeno-associated virus (AAV) capsid (AAV-Go.1) is closely related to the primate AAV-5 and has unique tropism and neutralization properties. J Virol 79, 15238-15245 (2005).
    • (2005) J Virol , vol.79 , pp. 15238-15245
    • Arbetman, A.E.1
  • 15
    • 77956810262 scopus 로고    scopus 로고
    • Prevalence and genetic diversity of adeno-associated viruses in bats from China
    • Li, Y. et al. Prevalence and genetic diversity of adeno-associated viruses in bats from China. J Gen Virol 91, 2601-2609 (2010).
    • (2010) J Gen Virol , vol.91 , pp. 2601-2609
    • Li, Y.1
  • 16
    • 80053965904 scopus 로고    scopus 로고
    • The fecal viral flora of California sea lions
    • Li, L. et al. The fecal viral flora of California sea lions. J Virol 85, 9909-9917 (2011).
    • (2011) J Virol , vol.85 , pp. 9909-9917
    • Li, L.1
  • 17
    • 84925966494 scopus 로고    scopus 로고
    • The X gene of adeno-associated virus 2 (AAV2) is involved in viral DNA replication
    • Cao, M., You, H. & Hermonat, P. L. The X gene of adeno-associated virus 2 (AAV2) is involved in viral DNA replication. PLos One 9, e104596 (2014).
    • (2014) PLos One , vol.9
    • Cao, M.1    You, H.2    Hermonat, P.L.3
  • 18
    • 77953439661 scopus 로고    scopus 로고
    • A viral assembly factor promotes AAV2 capsid formation in the nucleolus
    • Sonntag, F., Schmidt, K. & Kleinschmidt, J. A. A viral assembly factor promotes AAV2 capsid formation in the nucleolus. Proc Natl Acad Sci USA 107, 10220-10225 (2010).
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 10220-10225
    • Sonntag, F.1    Schmidt, K.2    Kleinschmidt, J.A.3
  • 19
    • 0029069597 scopus 로고
    • Minimum origin requirements for linear duplex AAV DNA replication in vitro
    • Ward, P. & Berns, K. I. Minimum origin requirements for linear duplex AAV DNA replication in vitro. Virology 209, 692-695 (1995).
    • (1995) Virology , vol.209 , pp. 692-695
    • Ward, P.1    Berns, K.I.2
  • 20
    • 0031016643 scopus 로고    scopus 로고
    • A novel 165-base-pair terminal repeat sequence is the sole cis requirement for the adenoassociated virus life cycle
    • Xiao, X., Xiao, W., Li, J. & Samulski, R. J. A novel 165-base-pair terminal repeat sequence is the sole cis requirement for the adenoassociated virus life cycle. J Virol 71, 941-948 (1997).
    • (1997) J Virol , vol.71 , pp. 941-948
    • Xiao, X.1    Xiao, W.2    Li, J.3    Samulski, R.J.4
  • 21
    • 0025214094 scopus 로고
    • Site-specific integration by adeno-associated virus
    • Kotin, R. M. et al. Site-specific integration by adeno-associated virus. Proc Natl Acad Sci USA 87, 2211-2215 (1990).
    • (1990) Proc Natl Acad Sci USA , vol.87 , pp. 2211-2215
    • Kotin, R.M.1
  • 22
    • 0026070440 scopus 로고
    • Targeted integration of adeno-associated virus (AAV) into human chromosome 19
    • Samulski, R. J. et al. Targeted integration of adeno-associated virus (AAV) into human chromosome 19. Embo J 10, 3941-3950 (1991).
    • (1991) Embo J , vol.10 , pp. 3941-3950
    • Samulski, R.J.1
  • 23
    • 0027092001 scopus 로고
    • Characterization of a preferred site on human chromosome 19q for integration of adenoassociated virus DNA by non-homologous recombination
    • Kotin, R. M., Linden, R. M. & Berns, K. I. Characterization of a preferred site on human chromosome 19q for integration of adenoassociated virus DNA by non-homologous recombination. Embo J 11, 5071-5078 (1992).
    • (1992) Embo J , vol.11 , pp. 5071-5078
    • Kotin, R.M.1    Linden, R.M.2    Berns, K.I.3
  • 24
    • 34249790547 scopus 로고    scopus 로고
    • Increased complexity of wild-type adeno-associated virus-chromosomal junctions as determined by analysis of unselected cellular genomes
    • Drew, H. R., Lockett, L. J. & Both, G. W. Increased complexity of wild-type adeno-associated virus-chromosomal junctions as determined by analysis of unselected cellular genomes. J Gen Virol 88, 1722-1732 (2007).
    • (2007) J Gen Virol , vol.88 , pp. 1722-1732
    • Drew, H.R.1    Lockett, L.J.2    Both, G.W.3
  • 25
    • 33747874648 scopus 로고    scopus 로고
    • Adeno-associated virus (AAV) capsid genes isolated from rat and mouse liver genomic DNA define two new AAV species distantly related to AAV-5
    • Lochrie, M. A. et al. Adeno-associated virus (AAV) capsid genes isolated from rat and mouse liver genomic DNA define two new AAV species distantly related to AAV-5. Virology 353, 68-82 (2006).
    • (2006) Virology , vol.353 , pp. 68-82
    • Lochrie, M.A.1
  • 26
    • 70449729753 scopus 로고    scopus 로고
    • Isolation and evaluation of novel adeno-associated virus sequences from porcine tissues
    • Bello, A. et al. Isolation and evaluation of novel adeno-associated virus sequences from porcine tissues. Gene Ther 16, 1320-1328 (2009).
    • (2009) Gene Ther , vol.16 , pp. 1320-1328
    • Bello, A.1
  • 28
    • 67349149598 scopus 로고    scopus 로고
    • A phylogeny of Diprotodontia (Marsupialia) based on sequences for five nuclear genes
    • Meredith, R. W., Westerman, M. & Springer, M. S. A phylogeny of Diprotodontia (Marsupialia) based on sequences for five nuclear genes. Mol Phylogenet Evol 51, 554-571 (2009).
    • (2009) Mol Phylogenet Evol , vol.51 , pp. 554-571
    • Meredith, R.W.1    Westerman, M.2    Springer, M.S.3
  • 29
    • 45949109669 scopus 로고    scopus 로고
    • MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences
    • Kumar, S., Nei, M., Dudley, J. & Tamura, K. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9, 299-306 (2008).
    • (2008) Brief Bioinform , vol.9 , pp. 299-306
    • Kumar, S.1    Nei, M.2    Dudley, J.3    Tamura, K.4
  • 30
    • 0345734253 scopus 로고    scopus 로고
    • Alternative polyadenylation of adeno-associated virus type 5 RNA within an internal intron is governed by both a downstream element within the intron 3' splice acceptor and an element upstream of the P41 initiation site
    • Qiu, J., Nayak, R. & Pintel, D. J. Alternative polyadenylation of adeno-associated virus type 5 RNA within an internal intron is governed by both a downstream element within the intron 3' splice acceptor and an element upstream of the P41 initiation site. J Virol 78, 83-93 (2004).
    • (2004) J Virol , vol.78 , pp. 83-93
    • Qiu, J.1    Nayak, R.2    Pintel, D.J.3
  • 31
    • 0032825452 scopus 로고    scopus 로고
    • Estimating transcription factor bindability on DNA
    • Tsunoda, T. & Takagi, T. Estimating transcription factor bindability on DNA. Bioinformatics 15, 622-630 (1999).
    • (1999) Bioinformatics , vol.15 , pp. 622-630
    • Tsunoda, T.1    Takagi, T.2
  • 32
    • 0024356710 scopus 로고
    • Adeno-associated virus P5 promoter contains an adenovirus E1A-inducible element and a binding site for the major late transcription factor
    • Chang, L. S., Shi, Y. & Shenk, T. Adeno-associated virus P5 promoter contains an adenovirus E1A-inducible element and a binding site for the major late transcription factor. J Virol 63, 3479-3488 (1989).
    • (1989) J Virol , vol.63 , pp. 3479-3488
    • Chang, L.S.1    Shi, Y.2    Shenk, T.3
  • 33
    • 0025943945 scopus 로고
    • Transcriptional repression by YY1, a human GLI-Kruppel-related protein, and relief of repression by adenovirus E1A protein
    • Shi, Y., Seto, E., Chang, L. S. & Shenk, T. Transcriptional repression by YY1, a human GLI-Kruppel-related protein, and relief of repression by adenovirus E1A protein. Cell 67, 377-388 (1991).
    • (1991) Cell , vol.67 , pp. 377-388
    • Shi, Y.1    Seto, E.2    Chang, L.S.3    Shenk, T.4
  • 34
    • 0023751447 scopus 로고
    • Synthesis of adeno-associated virus structural proteins requires both alternative mRNA splicing and alternative initiations from a single transcript
    • Becerra, S. P., Koczot, F., Fabisch, P. & Rose, J. A. Synthesis of adeno-associated virus structural proteins requires both alternative mRNA splicing and alternative initiations from a single transcript. J Virol 62, 2745-2754 (1988).
    • (1988) J Virol , vol.62 , pp. 2745-2754
    • Becerra, S.P.1    Koczot, F.2    Fabisch, P.3    Rose, J.A.4
  • 35
    • 0025218471 scopus 로고
    • Mutation of a consensus purine nucleotide binding site in the adeno-associated virus rep gene generates a dominant negative phenotype for DNA replication
    • Chejanovsky, N. & Carter, B. J. Mutation of a consensus purine nucleotide binding site in the adeno-associated virus rep gene generates a dominant negative phenotype for DNA replication. J Virol 64, 1764-1770 (1990).
    • (1990) J Virol , vol.64 , pp. 1764-1770
    • Chejanovsky, N.1    Carter, B.J.2
  • 36
    • 0025362618 scopus 로고
    • The AAV origin binding protein Rep68 is an ATP-dependent site-specific endonuclease with DNA helicase activity
    • Im, D. S. & Muzyczka, N. The AAV origin binding protein Rep68 is an ATP-dependent site-specific endonuclease with DNA helicase activity. Cell 61, 447-457 (1990).
    • (1990) Cell , vol.61 , pp. 447-457
    • Im, D.S.1    Muzyczka, N.2
  • 37
    • 0034099092 scopus 로고    scopus 로고
    • An adeno-associated virus (AAV) initiator protein, Rep78, catalyzes the cleavage and ligation of singlestranded AAV ori DNA
    • Smith, R. H. & Kotin, R. M. An adeno-associated virus (AAV) initiator protein, Rep78, catalyzes the cleavage and ligation of singlestranded AAV ori DNA. J Virol 74, 3122-3129 (2000).
    • (2000) J Virol , vol.74 , pp. 3122-3129
    • Smith, R.H.1    Kotin, R.M.2
  • 38
    • 0035875669 scopus 로고    scopus 로고
    • DNA helicase-mediated packaging of adeno-associated virus type 2 genomes into preformed capsids
    • King, J. A., Dubielzig, R., Grimm, D. & Kleinschmidt, J. A. DNA helicase-mediated packaging of adeno-associated virus type 2 genomes into preformed capsids. Embo J 20, 3282-3291 (2001).
    • (2001) Embo J , vol.20 , pp. 3282-3291
    • King, J.A.1    Dubielzig, R.2    Grimm, D.3    Kleinschmidt, J.A.4
  • 39
    • 0026748738 scopus 로고
    • Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria
    • Ilyina, T. V. & Koonin, E. V. Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria. Nucleic Acids Res 20, 3279-3285 (1992).
    • (1992) Nucleic Acids Res , vol.20 , pp. 3279-3285
    • Ilyina, T.V.1    Koonin, E.V.2
  • 40
    • 0036671409 scopus 로고    scopus 로고
    • Structural unity among viral origin binding proteins: Crystal structure of the nuclease domain of adeno-associated virus Rep
    • Hickman, A. B., Ronning, D. R., Kotin, R. M. & Dyda, F. Structural unity among viral origin binding proteins: crystal structure of the nuclease domain of adeno-associated virus Rep. Mol Cell 10, 327-337 (2002).
    • (2002) Mol Cell , vol.10 , pp. 327-337
    • Hickman, A.B.1    Ronning, D.R.2    Kotin, R.M.3    Dyda, F.4
  • 41
    • 13844254123 scopus 로고    scopus 로고
    • Binding and unwinding: SF3 viral helicases
    • Hickman, A. B. & Dyda, F. Binding and unwinding: SF3 viral helicases. Curr Opin Struct Biol 15, 77-85 (2005).
    • (2005) Curr Opin Struct Biol , vol.15 , pp. 77-85
    • Hickman, A.B.1    Dyda, F.2
  • 42
    • 0035431876 scopus 로고    scopus 로고
    • A viral phospholipase A2 is required for parvovirus infectivity
    • Zadori, Z. et al. A viral phospholipase A2 is required for parvovirus infectivity. Dev Cell 1, 291-302 (2001).
    • (2001) Dev Cell , vol.1 , pp. 291-302
    • Zadori, Z.1
  • 43
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J. D., Higgins, D. G. & Gibson, T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673-4680 (1994).
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 44
    • 84904815625 scopus 로고    scopus 로고
    • SWISS-MODEL: Modelling protein tertiary and quaternary structure using evolutionary information
    • Biasini, M. et al. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res 42, W252-258 (2014).
    • (2014) Nucleic Acids Res , vol.42 , pp. W252-258
    • Biasini, M.1
  • 45
    • 77957312097 scopus 로고    scopus 로고
    • Structures and functions of parvovirus capsids and the process of cell infection
    • Parrish, C. R. Structures and functions of parvovirus capsids and the process of cell infection. Curr Top Microbiol Immunol 343, 149-176 (2010).
    • (2010) Curr Top Microbiol Immunol , vol.343 , pp. 149-176
    • Parrish, C.R.1
  • 46
  • 47
    • 84869208042 scopus 로고    scopus 로고
    • Properties of the adeno-associated virus assembly-activating protein
    • Naumer, M. et al. Properties of the adeno-associated virus assembly-activating protein. J Virol 86, 13038-13048 (2012).
    • (2012) J Virol , vol.86 , pp. 13038-13048
    • Naumer, M.1
  • 48
    • 84952794406 scopus 로고    scopus 로고
    • Novel parvoviruses in reptiles and genome sequence of a lizard parvovirus shed light on Dependoparvovirus genus evolution
    • Penzes, J. J., Pham, H. T., Benko, M. & Tijssen, P. Novel parvoviruses in reptiles and genome sequence of a lizard parvovirus shed light on Dependoparvovirus genus evolution. J Gen Virol 96, 2769-2779 (2015).
    • (2015) J Gen Virol , vol.96 , pp. 2769-2779
    • Penzes, J.J.1    Pham, H.T.2    Benko, M.3    Tijssen, P.4
  • 49
    • 0033621180 scopus 로고    scopus 로고
    • SINEs of the perfect character
    • Hillis, D. M. SINEs of the perfect character. Proc Natl Acad Sci USA 96, 9979-9981 (1999).
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 9979-9981
    • Hillis, D.M.1
  • 50
    • 77955027318 scopus 로고    scopus 로고
    • Tracking marsupial evolution using archaic genomic retroposon insertions
    • Nilsson, M. A. et al. Tracking marsupial evolution using archaic genomic retroposon insertions. PLos Biol 8, e1000436 (2010).
    • (2010) PLos Biol , vol.8
    • Nilsson, M.A.1
  • 51
    • 0042718469 scopus 로고    scopus 로고
    • Molecular evidence for the last survivor of an ancient kangaroo lineage
    • Westerman, M. et al. Molecular evidence for the last survivor of an ancient kangaroo lineage. J Mamm Evol 9, 209-223 (2002).
    • (2002) J Mamm Evol , vol.9 , pp. 209-223
    • Westerman, M.1
  • 52
    • 63149179208 scopus 로고    scopus 로고
    • A phylogeny and timescale for the living genera of kangaroos and kin (Macropodiformes : Marsupialia) based on nuclear DNA sequences
    • Meredith, R. W., Westerman, M. & Springer, M. S. A phylogeny and timescale for the living genera of kangaroos and kin (Macropodiformes : Marsupialia) based on nuclear DNA sequences. Aust J Zool 56, 395-410 (2008).
    • (2008) Aust J Zool , vol.56 , pp. 395-410
    • Meredith, R.W.1    Westerman, M.2    Springer, M.S.3
  • 53
    • 0024307824 scopus 로고
    • Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea
    • Kishino, H. & Hasegawa, M. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J Mol Evol 29, 170-179 (1989).
    • (1989) J Mol Evol , vol.29 , pp. 170-179
    • Kishino, H.1    Hasegawa, M.2
  • 54
    • 0032766857 scopus 로고    scopus 로고
    • Multiple comparisons of log-likelihoods with applications to phylogenetic inference
    • Shimodaira, H. & Hasegawa, M. 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
  • 55
    • 84908162664 scopus 로고    scopus 로고
    • Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum
    • Gatesy, J. & Springer, M. S. Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. Mol Phylogenet Evol 80, 231-266 (2014).
    • (2014) Mol Phylogenet Evol , vol.80 , pp. 231-266
    • Gatesy, J.1    Springer, M.S.2
  • 56
    • 0032148637 scopus 로고    scopus 로고
    • The phylogenetic position of the musky rat-kangaroo and the evolution of bipedal hopping in kangaroos (Macropodidae: Diprotodontia)
    • Burk, A., Westerman, M. & Springer, M. The phylogenetic position of the musky rat-kangaroo and the evolution of bipedal hopping in kangaroos (Macropodidae: Diprotodontia). Syst Biol 47, 457-474 (1998).
    • (1998) Syst Biol , vol.47 , pp. 457-474
    • Burk, A.1    Westerman, M.2    Springer, M.3
  • 57
    • 39249084537 scopus 로고    scopus 로고
    • A phylogeny and timescale for marsupial evolution based on sequences for five nuclear genes
    • Meredith, R. W., Westerman, M., Case, J. A. & Springer, M. S. A phylogeny and timescale for marsupial evolution based on sequences for five nuclear genes. J Mamm Evol 15, 1-36 (2008).
    • (2008) J Mamm Evol , vol.15 , pp. 1-36
    • Meredith, R.W.1    Westerman, M.2    Case, J.A.3    Springer, M.S.4
  • 59
    • 77953665114 scopus 로고    scopus 로고
    • Filoviruses are ancient and integrated into mammalian genomes
    • Taylor, D. J., Leach, R. W. & Bruenn, J. Filoviruses are ancient and integrated into mammalian genomes. BMC Evol Biol 10, 193 (2010).
    • (2010) BMC Evol Biol , vol.10 , pp. 193
    • Taylor, D.J.1    Leach, R.W.2    Bruenn, J.3
  • 60
    • 84884518363 scopus 로고    scopus 로고
    • Selectively maintained paleoviruses in Holarctic water fleas reveal an ancient origin for phleboviruses
    • Ballinger, M. J., Bruenn, J. A., Kotov, A. A. & Taylor, D. J. Selectively maintained paleoviruses in Holarctic water fleas reveal an ancient origin for phleboviruses. Virology 446, 276-282 (2013).
    • (2013) Virology , vol.446 , pp. 276-282
    • Ballinger, M.J.1    Bruenn, J.A.2    Kotov, A.A.3    Taylor, D.J.4
  • 61
    • 0037377762 scopus 로고    scopus 로고
    • Molecular clocks and the puzzle of RNA virus origins
    • Holmes, E. C. Molecular clocks and the puzzle of RNA virus origins. J Virol 77, 3893-3897 (2003).
    • (2003) J Virol , vol.77 , pp. 3893-3897
    • Holmes, E.C.1
  • 63
    • 84867218805 scopus 로고    scopus 로고
    • Paleovirology and virally derived immunity
    • Aswad, A. & Katzourakis, A. Paleovirology and virally derived immunity. Trends Ecol Evol 27, 627-636 (2012).
    • (2012) Trends Ecol Evol , vol.27 , pp. 627-636
    • Aswad, A.1    Katzourakis, A.2
  • 64
    • 77049085764 scopus 로고    scopus 로고
    • (ed. Saif, Y. M.) Ch. 13 - Viral Infections in Waterfowl, Blackwell Publishing
    • Gough, R. E. In Diseases of Poultry (ed. Saif, Y. M.) Ch. 13 - Viral Infections in Waterfowl, 397-404 (Blackwell Publishing, 2008).
    • (2008) Diseases of Poultry , pp. 397-404
    • Gough, R.E.1
  • 65
    • 0032036690 scopus 로고    scopus 로고
    • Fv1 the mouse retrovirus resistance gene
    • Stoye, J. P. Fv1, the mouse retrovirus resistance gene. Rev Sci Tech 17, 269-277 (1998).
    • (1998) Rev Sci Tech , vol.17 , pp. 269-277
    • Stoye, J.P.1
  • 66
    • 80054890343 scopus 로고    scopus 로고
    • The evolution of endogenous viral elements
    • Holmes, E. C. The evolution of endogenous viral elements. Cell Host Microbe 10, 368-377 (2011).
    • (2011) Cell Host Microbe , vol.10 , pp. 368-377
    • Holmes, E.C.1
  • 67
    • 84858429240 scopus 로고    scopus 로고
    • Endogenous viruses: Insights into viral evolution and impact on host biology
    • Feschotte, C. & Gilbert, C. Endogenous viruses: insights into viral evolution and impact on host biology. Nat Rev Genet 13, 283-296 (2012).
    • (2012) Nat Rev Genet , vol.13 , pp. 283-296
    • Feschotte, C.1    Gilbert, C.2
  • 68
    • 84898672434 scopus 로고    scopus 로고
    • Paleovirology of 'syncytins', retroviral env genes exapted for a role in placentation
    • Lavialle, C. et al. Paleovirology of 'syncytins', retroviral env genes exapted for a role in placentation. Philos Trans R Soc Lond B Biol Sci 368, 20120507 (2013).
    • (2013) Philos Trans R Soc Lond B Biol Sci , vol.368
    • Lavialle, C.1
  • 69
    • 0001525977 scopus 로고
    • The average number of generations until fixation of a mutant gene in a finite population
    • Kimura, M. & Ohta, T. The average number of generations until fixation of a mutant gene in a finite population. Genetics 61, 763-771 (1969).
    • (1969) Genetics , vol.61 , pp. 763-771
    • Kimura, M.1    Ohta, T.2
  • 70
    • 45249106003 scopus 로고    scopus 로고
    • Near neutrality: Leading edge of the neutral theory of molecular evolution
    • Hughes, A. L. Near neutrality: leading edge of the neutral theory of molecular evolution. Ann N Y Acad Sci 1133, 162-179 (2008).
    • (2008) Ann N y Acad Sci , vol.1133 , pp. 162-179
    • Hughes, A.L.1
  • 71
    • 84866121642 scopus 로고    scopus 로고
    • Weak selection and protein evolution
    • Akashi, H., Osada, N. & Ohta, T. Weak selection and protein evolution. Genetics 192, 15-31 (2012).
    • (2012) Genetics , vol.192 , pp. 15-31
    • Akashi, H.1    Osada, N.2    Ohta, T.3
  • 72
    • 84862535419 scopus 로고    scopus 로고
    • Population growth enhances the mean fixation time of neutral mutations and the persistence of neutral variation
    • Waxman, D. Population growth enhances the mean fixation time of neutral mutations and the persistence of neutral variation. Genetics 191, 561-577 (2012).
    • (2012) Genetics , vol.191 , pp. 561-577
    • Waxman, D.1
  • 73
    • 41149127909 scopus 로고    scopus 로고
    • Rinderpest. Driven to extinction
    • Normile, D. Rinderpest. Driven to extinction. Science 319, 1606-1609 (2008).
    • (2008) Science , vol.319 , pp. 1606-1609
    • Normile, D.1
  • 74
    • 73849140080 scopus 로고    scopus 로고
    • Endogenous non-retroviral RNA virus elements in mammalian genomes
    • Horie, M. et al. Endogenous non-retroviral RNA virus elements in mammalian genomes. Nature 463, 84-87 (2010).
    • (2010) Nature , vol.463 , pp. 84-87
    • Horie, M.1
  • 75
    • 0002352391 scopus 로고
    • In History of Australian Vegetation: Cretaceous to Recent
    • (ed. Hill, R. S.) Ch. 16, Cambridge University Press
    • Hill, R. S. In History of Australian Vegetation: Cretaceous to Recent (ed. Hill, R. S.) Ch. 16 - The History of Selected Australian Taxa, 390-419 (Cambridge University Press, 1994).
    • (1994) The History of Selected Australian Taxa , pp. 390-419
    • Hill, R.S.1
  • 76
    • 33747611954 scopus 로고    scopus 로고
    • Cenozoic climatic change and the development of the arid vegetation in Australia
    • Martin, H. A. Cenozoic climatic change and the development of the arid vegetation in Australia. J Arid Environ 66, 553-563 (2006).
    • (2006) J Arid Environ , vol.66 , pp. 553-563
    • Martin, H.A.1
  • 77
    • 84949085624 scopus 로고    scopus 로고
    • AAV ancestral reconstruction library enables selection of broadly infectious viral variants
    • Santiago-Ortiz, J. et al. AAV ancestral reconstruction library enables selection of broadly infectious viral variants. Gene Ther 22, 934-946 (2015).
    • (2015) Gene Ther , vol.22 , pp. 934-946
    • Santiago-Ortiz, J.1
  • 78
    • 84947022242 scopus 로고    scopus 로고
    • In silico reconstruction of the viral evolutionary lineage yields a potent gene therapy vector
    • Zinn, E. et al. In silico reconstruction of the viral evolutionary lineage yields a potent gene therapy vector. Cell Rep 12, 1056-1068 (2015).
    • (2015) Cell Rep , vol.12 , pp. 1056-1068
    • Zinn, E.1
  • 79
    • 84890330527 scopus 로고    scopus 로고
    • MEGA6: Molecular Evolutionary Genetics Analysis version 6.0
    • Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30, 2725-2729 (2013).
    • (2013) Mol Biol Evol , vol.30 , pp. 2725-2729
    • Tamura, K.1    Stecher, G.2    Peterson, D.3    Filipski, A.4    Kumar, S.5
  • 80
    • 13244255415 scopus 로고    scopus 로고
    • MUSCLE: A multiple sequence alignment method with reduced time and space complexity
    • Edgar, R. C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5, 113 (2004).
    • (2004) BMC Bioinformatics , vol.5 , pp. 113
    • Edgar, R.C.1
  • 81
    • 84977278047 scopus 로고    scopus 로고
    • Ch. 11 - Working with Various Computer Platforms, Sinauer Associates, Inc
    • Hall, B. G. Phylogenetic Trees Made Easy: A How-To Manual. Ch. 11 - Working with Various Computer Platforms, 161-176 (Sinauer Associates, Inc., 2011).
    • (2011) Phylogenetic Trees Made Easy: A How-To Manual , pp. 161-176
    • Hall, B.G.1
  • 82
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2-approximately maximum-likelihood trees for large alignments
    • Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2-approximately maximum-likelihood trees for large alignments. PLos One 5, e9490 (2010).
    • (2010) PLos One , vol.5
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 83
    • 77958523684 scopus 로고    scopus 로고
    • Cytogenetics meets phylogenetics: A review of karyotype evolution in diprotodontian marsupials
    • Westerman, M., Meredith, R. W. & Springer, M. S. Cytogenetics meets phylogenetics: a review of karyotype evolution in diprotodontian marsupials. J Hered 101, 690-702 (2010).
    • (2010) J Hered , vol.101 , pp. 690-702
    • Westerman, M.1    Meredith, R.W.2    Springer, M.S.3
  • 84
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690 (2006).
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 86
    • 84860109324 scopus 로고    scopus 로고
    • MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space
    • Ronquist, F. et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61, 539-542 (2012).
    • (2012) Syst Biol , vol.61 , pp. 539-542
    • Ronquist, F.1
  • 87
    • 45849154165 scopus 로고    scopus 로고
    • JModelTest: Phylogenetic model averaging
    • Posada, D. jModelTest: phylogenetic model averaging. Mol Biol Evol 25, 1253-1256 (2008).
    • (2008) Mol Biol Evol , vol.25 , pp. 1253-1256
    • Posada, D.1
  • 88
    • 33748780649 scopus 로고    scopus 로고
    • Is there a star tree paradox?
    • Kolaczkowski, B. & Thornton, J. W. Is there a star tree paradox? Mol Biol Evol 23, 1819-1823 (2006).
    • (2006) Mol Biol Evol , vol.23 , pp. 1819-1823
    • Kolaczkowski, B.1    Thornton, J.W.2
  • 89
    • 13444307044 scopus 로고    scopus 로고
    • Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
    • Krissinel, E. & Henrick, K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 60, 2256-2268 (2004).
    • (2004) Acta Crystallogr D Biol Crystallogr , vol.60 , pp. 2256-2268
    • Krissinel, E.1    Henrick, K.2
  • 90
    • 33751210120 scopus 로고    scopus 로고
    • Structurally mapping the diverse phenotype of adeno-associated virus serotype 4
    • Govindasamy, L. et al. Structurally mapping the diverse phenotype of adeno-associated virus serotype 4. J Virol 80, 11556-11570 (2006).
    • (2006) J Virol , vol.80 , pp. 11556-11570
    • Govindasamy, L.1
  • 91
    • 13244281317 scopus 로고    scopus 로고
    • Coot: Model-building tools for molecular graphics
    • Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60, 2126-2132 (2004).
    • (2004) Acta Crystallogr D Biol Crystallogr , vol.60 , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2
  • 92
    • 58149182734 scopus 로고    scopus 로고
    • VIPERdb2: An enhanced and web API enabled relational database for structural virology
    • Carrillo-Tripp, M. et al. VIPERdb2: an enhanced and web API enabled relational database for structural virology. Nucleic Acids Res 37, D436-442 (2009).
    • (2009) Nucleic Acids Res , vol.37 , pp. D436-442
    • Carrillo-Tripp, M.1
  • 94
    • 0041630781 scopus 로고    scopus 로고
    • Crystal structure of the SF3 helicase from adeno-associated virus type 2
    • James, J. A. et al. Crystal structure of the SF3 helicase from adeno-associated virus type 2. Structure 11, 1025-1035 (2003).
    • (2003) Structure , vol.11 , pp. 1025-1035
    • James, J.A.1
  • 95
    • 0036678455 scopus 로고    scopus 로고
    • The atomic structure of adeno-associated virus (AAV-2), a vector for human gene therapy
    • Xie, Q. et al. The atomic structure of adeno-associated virus (AAV-2), a vector for human gene therapy. Proc Natl Acad Sci USA 99, 10405-10410 (2002).
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 10405-10410
    • Xie, Q.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.