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Volumn 13, Issue 2, 2017, Pages

Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families

Author keywords

[No Author keywords available]

Indexed keywords

ADENOVIRIDAE; ARTICLE; COMPARATIVE STUDY; FREQUENCY; GENETIC VARIABILITY; HEPADNAVIRIDAE; NONHUMAN; PAPILLOMAVIRIDAE; PHYLOGENY; POLYOMAVIRIDAE; POXVIRIDAE; RHABDOVIRIDAE; VIRUS TRANSMISSION; ANIMAL; GENETICS; HOST RANGE; HUMAN; MOLECULAR EVOLUTION; VIRUS; VIRUS GENOME; ZOONOSIS;

EID: 85014111455     PISSN: 15537366     EISSN: 15537374     Source Type: Journal    
DOI: 10.1371/journal.ppat.1006215     Document Type: Article
Times cited : (184)

References (47)
  • 1
    • 11144244968 scopus 로고    scopus 로고
    • Integrating reptilian herpesviruses into the family herpesviridae
    • 5613300, Epub 2004/12/23
    • McGeoch DJ, Gatherer D, Integrating reptilian herpesviruses into the family herpesviridae. Journal of virology. 2005;79(2):725–31. Epub 2004/12/23. doi: 10.1128/JVI.79.2.725-731.200515613300
    • (2005) Journal of virology , vol.79 , Issue.2 , pp. 725-731
    • McGeoch, D.J.1    Gatherer, D.2
  • 3
    • 0034691154 scopus 로고    scopus 로고
    • Acute and persistent viral life strategies and their relationship to emerging diseases
    • 087374
    • Villarreal LP, Defilippis VR, Gottlieb KA, Acute and persistent viral life strategies and their relationship to emerging diseases. Virology. 2000;272(1):1–6. doi: 10.1006/viro.2000.038110873743
    • (2000) Virology , vol.272 , Issue.1 , pp. 1-6
    • Villarreal, L.P.1    Defilippis, V.R.2    Gottlieb, K.A.3
  • 5
    • 84963722864 scopus 로고    scopus 로고
    • Virological factors that increase the transmissibility of emerging human viruses
    • 700184
    • Geoghegan JL, Senior AM, Di Giallonardo F, Holmes EC, Virological factors that increase the transmissibility of emerging human viruses. Proc Natl Acad Sci USA. 2016;113(15):4170–5. doi: 10.1073/pnas.152158211327001840
    • (2016) Proc Natl Acad Sci USA , vol.113 , Issue.15 , pp. 4170-4175
    • Geoghegan, J.L.1    Senior, A.M.2    Di Giallonardo, F.3    Holmes, E.C.4
  • 6
    • 84920422621 scopus 로고    scopus 로고
    • The evolution and emergence of hantaviruses
    • 5562117,.;: –. Epub 2015/01/07
    • Holmes EC, Zhang YZ, The evolution and emergence of hantaviruses. Current opinion in virology. 2015;10:27–33. Epub 2015/01/07. doi: 10.1016/j.coviro.2014.12.00725562117
    • (2015) Current opinion in virology , vol.10 , pp. 27-33
    • Holmes, E.C.1    Zhang, Y.Z.2
  • 7
    • 1242284669 scopus 로고    scopus 로고
    • A cophylogenetic perspective of RNA-virus evolution
    • 2949128, Epub 2003/09/02
    • Jackson AP, Charleston MA, A cophylogenetic perspective of RNA-virus evolution. Molecular biology and evolution. 2004;21(1):45–57. Epub 2003/09/02. doi: 10.1093/molbev/msg23212949128
    • (2004) Molecular biology and evolution , vol.21 , Issue.1 , pp. 45-57
    • Jackson, A.P.1    Charleston, M.A.2
  • 8
    • 78651065709 scopus 로고    scopus 로고
    • Family level phylogenies reveal modes of macroevolution in RNA viruses
    • 117325
    • Kitchen A, Shackelton LA, Holmes EC, Family level phylogenies reveal modes of macroevolution in RNA viruses. Proc Natl Acad Sci USA. 2011;108(1):238–43. doi: 10.1073/pnas.101109010821173251
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.1 , pp. 238-243
    • Kitchen, A.1    Shackelton, L.A.2    Holmes, E.C.3
  • 9
    • 84985898228 scopus 로고    scopus 로고
    • Pathogen population bottlenecks and adaptive landscapes: overcoming the barriers to disease emergence
    • Geoghegan JL, Senior AM, Holmes EC, Pathogen population bottlenecks and adaptive landscapes: overcoming the barriers to disease emergence. Proc R Soc Lond B. 2016;283(1837).
    • (2016) Proc R Soc Lond B , vol.283 , Issue.1837
    • Geoghegan, J.L.1    Senior, A.M.2    Holmes, E.C.3
  • 10
    • 84919663851 scopus 로고    scopus 로고
    • Early mesozoic coexistence of amniotes and hepadnaviridae
    • 5501991,..; ():
    • Suh A, Weber CC, Kehlmaier C, Braun EL, Green RE, Fritz U, et al. Early mesozoic coexistence of amniotes and hepadnaviridae. PLoS Genet. 2014;10(12):e1004559. doi: 10.1371/journal.pgen.100455925501991
    • (2014) PLoS Genet , vol.10 , Issue.12 , pp. e1004559
    • Suh, A.1    Weber, C.C.2    Kehlmaier, C.3    Braun, E.L.4    Green, R.E.5    Fritz, U.6
  • 11
    • 84983479595 scopus 로고    scopus 로고
    • Distinct viral lineages from fish and amphibians reveal the complex evolutionary history of hepadnaviruses
    • 7334580, Epub 2016/06/24
    • Dill JA, Camus AC, Leary JH, Di Giallonardo F, Holmes EC, Ng TF, Distinct viral lineages from fish and amphibians reveal the complex evolutionary history of hepadnaviruses. Journal of virology. 2016;90(17):7920–33. Epub 2016/06/24. doi: 10.1128/JVI.00832-1627334580
    • (2016) Journal of virology , vol.90 , Issue.17 , pp. 7920-7933
    • Dill, J.A.1    Camus, A.C.2    Leary, J.H.3    Di Giallonardo, F.4    Holmes, E.C.5    Ng, T.F.6
  • 13
    • 84886058591 scopus 로고    scopus 로고
    • Absence of frequent herpesvirus transmission in a nonhuman primate predator-prey system in the wild
    • 3885068, Epub 2013/07/26
    • Murthy S, Couacy-Hymann E, Metzger S, Nowak K, De Nys H, Boesch C, et al. Absence of frequent herpesvirus transmission in a nonhuman primate predator-prey system in the wild. Journal of virology. 2013;87(19):10651–9. Epub 2013/07/26. doi: 10.1128/JVI.01104-1323885068
    • (2013) Journal of virology , vol.87 , Issue.19 , pp. 10651-10659
    • Murthy, S.1    Couacy-Hymann, E.2    Metzger, S.3    Nowak, K.4    De Nys, H.5    Boesch, C.6
  • 14
    • 0002393841 scopus 로고
    • The use of tree comparison metrics
    • Penny D, Hendy MD, The use of tree comparison metrics. Systematic biology. 1985;34(1):75–82.
    • (1985) Systematic biology , vol.34 , Issue.1 , pp. 75-82
    • Penny, D.1    Hendy, M.D.2
  • 16
    • 16244383582 scopus 로고    scopus 로고
    • Reconstruction of the cophylogenetic history of related phylogenetic trees with divergence timing information
    • 820286
    • Merkle D, Middendorf M, Reconstruction of the cophylogenetic history of related phylogenetic trees with divergence timing information. Theory in Biosciences. 2005;123(4):277–99. doi: 10.1016/j.thbio.2005.01.00318202869
    • (2005) Theory in Biosciences , vol.123 , Issue.4 , pp. 277-299
    • Merkle, D.1    Middendorf, M.2
  • 17
    • 84939515457 scopus 로고    scopus 로고
    • Time scale evolution of avipoxviruses
    • 6231721,.;: –
    • Le Loc’h G, Bertagnoli S, Ducatez MF, Time scale evolution of avipoxviruses. Infect Genet Evol. 2015;35:75–81. doi: 10.1016/j.meegid.2015.07.03126231721
    • (2015) Infect Genet Evol , vol.35 , pp. 75-81
    • Le Loc’h, G.1    Bertagnoli, S.2    Ducatez, M.F.3
  • 19
    • 81755165762 scopus 로고    scopus 로고
    • Evaluating the evidence for virus/host co-evolution
    • 2440848, Epub 2012/03/24
    • Sharp PM, Simmonds P, Evaluating the evidence for virus/host co-evolution. Current opinion in virology. 2011;1(5):436–41. Epub 2012/03/24. doi: 10.1016/j.coviro.2011.10.01822440848
    • (2011) Current opinion in virology , vol.1 , Issue.5 , pp. 436-441
    • Sharp, P.M.1    Simmonds, P.2
  • 20
    • 84858960202 scopus 로고    scopus 로고
    • Convergent evolution of escape from hepaciviral antagonism in primates
    • 2427742,.; ():
    • Patel MR, Loo Y-M, Horner SM, Gale M, Jr.Malik HS, Convergent evolution of escape from hepaciviral antagonism in primates. PLoS Biol. 2012;10(3):e1001282. doi: 10.1371/journal.pbio.100128222427742
    • (2012) PLoS Biol , vol.10 , Issue.3 , pp. e1001282
    • Patel, M.R.1    Loo, Y.-M.2    Horner, S.M.3    Gale, M.4    Malik, H.S.5
  • 21
    • 0032873055 scopus 로고    scopus 로고
    • Phylogenetic analysis of GB viruses A and C: evidence for cospeciation between virus isolates and their primate hosts
    • 0501484,.;: –. Epub 1999/09/29
    • Charrel RN, De Micco P, de Lamballerie X, Phylogenetic analysis of GB viruses A and C: evidence for cospeciation between virus isolates and their primate hosts. The Journal of general virology. 1999;80:2329–35. Epub 1999/09/29. doi: 10.1099/0022-1317-80-9-232910501484
    • (1999) The Journal of general virology , vol.80 , pp. 2329-2335
    • Charrel, R.N.1    De Micco, P.2    de Lamballerie, X.3
  • 25
    • 77956685623 scopus 로고    scopus 로고
    • Island biogeography reveals the deep history of SIV
    • 0847261,..; (): -
    • Worobey M, Telfer P, Souquière S, Hunter M, Coleman CA, Metzger MJ, et al. Island biogeography reveals the deep history of SIV. Science. 2010;329(5998):1487-. doi: 10.1126/science.119355020847261
    • (2010) Science , vol.329 , Issue.5998 , pp. 1487
    • Worobey, M.1    Telfer, P.2    Souquière, S.3    Hunter, M.4    Coleman, C.A.5    Metzger, M.J.6
  • 28
    • 0036623490 scopus 로고    scopus 로고
    • Preferential host switching by primate lentiviruses can account for phylogenetic similarity with the primate phylogeny
    • 2079649, Epub 2002/06/25
    • Charleston MA, Robertson DL, Preferential host switching by primate lentiviruses can account for phylogenetic similarity with the primate phylogeny. Systematic biology. 2002;51(3):528–35. Epub 2002/06/25. doi: 10.1080/1063515029006994012079649
    • (2002) Systematic biology , vol.51 , Issue.3 , pp. 528-535
    • Charleston, M.A.1    Robertson, D.L.2
  • 30
    • 84964699856 scopus 로고    scopus 로고
    • Substitution model adequacy and assessing the reliability of estimates of virus evolutionary rates and time scales
    • 641698
    • Duchêne S, Di Giallonardo F, Holmes EC, Substitution model adequacy and assessing the reliability of estimates of virus evolutionary rates and time scales. Molecular biology and evolution. 2015;33(1):255–67. doi: 10.1093/molbev/msv20726416981
    • (2015) Molecular biology and evolution , vol.33 , Issue.1 , pp. 255-267
    • Duchêne, S.1    Di Giallonardo, F.2    Holmes, E.C.3
  • 32
    • 84958212147 scopus 로고    scopus 로고
    • Seqotron: a user-friendly sequence editor for Mac OS X
    • 6887850,.;:. Epub 2016/02/19
    • Fourment M, Holmes EC, Seqotron: a user-friendly sequence editor for Mac OS X. BMC research notes. 2016;9:106. Epub 2016/02/19. doi: 10.1186/s13104-016-1927-426887850
    • (2016) BMC research notes , vol.9 , pp. 106
    • Fourment, M.1    Holmes, E.C.2
  • 33
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • 503414
    • Edgar RC, MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792–7. doi: 10.1093/nar/gkh34015034147
    • (2004) Nucleic Acids Res , vol.32 , Issue.5 , pp. 1792-1797
    • Edgar, R.C.1
  • 34
    • 67650757433 scopus 로고    scopus 로고
    • trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
    • 9505945, Epub 2009/06/10
    • Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T, trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25(15):1972–3. Epub 2009/06/10. doi: 10.1093/bioinformatics/btp34819505945
    • (2009) Bioinformatics , vol.25 , Issue.15 , pp. 1972-1973
    • Capella-Gutierrez, S.1    Silla-Martinez, J.M.2    Gabaldon, T.3
  • 35
    • 13844275303 scopus 로고    scopus 로고
    • Recombination Analysis Tool (RAT): a program for the high-throughput detection of recombination
    • 533346
    • Etherington GJ, Dicks J, Roberts IN, Recombination Analysis Tool (RAT): a program for the high-throughput detection of recombination. Bioinformatics. 2005;21(3):278–81. doi: 10.1093/bioinformatics/bth50015333462
    • (2005) Bioinformatics , vol.21 , Issue.3 , pp. 278-281
    • Etherington, G.J.1    Dicks, J.2    Roberts, I.N.3
  • 36
    • 33645816587 scopus 로고    scopus 로고
    • Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified
    • 6563161,.;:. Epub 2006/03/28
    • Keane TM, Creevey CJ, Pentony MM, Naughton TJ, McLnerney JO, Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC evolutionary biology. 2006;6:29. Epub 2006/03/28. doi: 10.1186/1471-2148-6-2916563161
    • (2006) BMC evolutionary biology , vol.6 , pp. 29
    • Keane, T.M.1    Creevey, C.J.2    Pentony, M.M.3    Naughton, T.J.4    McLnerney, J.O.5
  • 37
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
    • 0525638, Epub 2010/06/09
    • Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O, New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic biology. 2010;59(3):307–21. Epub 2010/06/09. doi: 10.1093/sysbio/syq01020525638
    • (2010) Systematic biology , vol.59 , Issue.3 , pp. 307-321
    • Guindon, S.1    Dufayard, J.F.2    Lefort, V.3    Anisimova, M.4    Hordijk, W.5    Gascuel, O.6
  • 38
    • 33745256005 scopus 로고    scopus 로고
    • Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative
    • 6785212, Epub 2006/06/21
    • Anisimova M, Gascuel O, Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Systematic biology. 2006;55(4):539–52. Epub 2006/06/21. doi: 10.1080/1063515060075545316785212
    • (2006) Systematic biology , vol.55 , Issue.4 , pp. 539-552
    • Anisimova, M.1    Gascuel, O.2
  • 39
    • 80052014395 scopus 로고    scopus 로고
    • Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes
    • 154040
    • Anisimova M, Gil M, Dufayard J-F, Dessimoz C, Gascuel O, Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Systematic biology. 2011;60(5):685–99. doi: 10.1093/sysbio/syr04121540409
    • (2011) Systematic biology , vol.60 , Issue.5 , pp. 685-699
    • Anisimova, M.1    Gil, M.2    Dufayard, J.-F.3    Dessimoz, C.4    Gascuel, O.5
  • 40
    • 84944911288 scopus 로고    scopus 로고
    • A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
    • 644423
    • Prum RO, Berv JS, Dornburg A, Field DJ, Townsend JP, Lemmon EM, et al. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature. 2015;526(7574):569–73. doi: 10.1038/nature1569726444237
    • (2015) Nature , vol.526 , Issue.7574 , pp. 569-573
    • Prum, R.O.1    Berv, J.S.2    Dornburg, A.3    Field, D.J.4    Townsend, J.P.5    Lemmon, E.M.6
  • 43
    • 84866289853 scopus 로고    scopus 로고
    • Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
    • Song S, Liu L, Edwards SV, Wu S, Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proceedings of the National Academy of Sciences. 2012;109(37):14942–7.
    • (2012) Proceedings of the National Academy of Sciences , vol.109 , Issue.37 , pp. 14942-14947
    • Song, S.1    Liu, L.2    Edwards, S.V.3    Wu, S.4
  • 45
    • 84931824945 scopus 로고    scopus 로고
    • Simulating and detecting autocorrelation of molecular evolutionary rates among lineages
    • 5155426, Epub 2014/08/27
    • Ho SYW, Duchene S, Duchene D, Simulating and detecting autocorrelation of molecular evolutionary rates among lineages. Molecular ecology resources. 2015;15(4):688–96. Epub 2014/08/27. doi: 10.1111/1755-0998.1232025155426
    • (2015) Molecular ecology resources , vol.15 , Issue.4 , pp. 688-696
    • Ho, S.Y.W.1    Duchene, S.2    Duchene, D.3
  • 46
    • 12044252586 scopus 로고
    • Distributions of tree comparison metrics—some new results
    • Steel MA, Penny D, Distributions of tree comparison metrics—some new results. Systematic biology. 1993;42(2):126–41.
    • (1993) Systematic biology , vol.42 , Issue.2 , pp. 126-141
    • Steel, M.A.1    Penny, D.2
  • 47
    • 85014121158 scopus 로고    scopus 로고
    • harleston MA. TreeMap 2011
    • Charleston MA. TreeMap 2011. https://sites.google.com/site/cophylogeny/home.


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