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Volumn 112, Issue 2, 2015, Pages 464-469

Pan-vertebrate comparative genomics unmasks retrovirus macroevolution

Author keywords

Endogenous retrovirus; Evolution; Phylogenetics; Retrovirus; Transmission

Indexed keywords

HOST FACTOR; VIRUS DNA;

EID: 84920982305     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1414980112     Document Type: Article
Times cited : (124)

References (43)
  • 3
    • 33745972414 scopus 로고    scopus 로고
    • Retroviral invasion of the koala genome
    • Tarlinton RE, Meers J, Young PR (2006) Retroviral invasion of the koala genome. Nature 442(7098):79-81.
    • (2006) Nature , vol.442 , Issue.7098 , pp. 79-81
    • Tarlinton, R.E.1    Meers, J.2    Young, P.R.3
  • 4
    • 77956477507 scopus 로고    scopus 로고
    • The evolution of HIV-1 and the origin of AIDS
    • Sharp PM, Hahn BH (2010) The evolution of HIV-1 and the origin of AIDS. Philos Trans R Soc Lond B Biol Sci 365(1552):2487-2494.
    • (2010) Philos Trans R Soc Lond B Biol Sci , vol.365 , Issue.1552 , pp. 2487-2494
    • Sharp, P.M.1    Hahn, B.H.2
  • 5
    • 0002075936 scopus 로고    scopus 로고
    • Retrotransposons, Endogenous Retroviruses, and the Evolution of Retroelements
    • eds Coffin JM, Hughes SH, Varmus HE (Cold Spring Harbor Lab Press, Cold Spring Harbor, NY)
    • Boeke JD, Stoye JP (1997) Retrotransposons, Endogenous Retroviruses, and the Evolution of Retroelements. Retroviruses, eds Coffin JM, Hughes SH, Varmus HE (Cold Spring Harbor Lab Press, Cold Spring Harbor, NY), pp 343-436.
    • (1997) Retroviruses , pp. 343-436
    • Boeke, J.D.1    Stoye, J.P.2
  • 6
    • 84898675328 scopus 로고    scopus 로고
    • Identification of an ancient endogenous retrovirus, predating the divergence of the placental mammals
    • Lee A, Nolan A, Watson J, Tristem M (2013) Identification of an ancient endogenous retrovirus, predating the divergence of the placental mammals. Philos Trans R Soc Lond B Biol Sci 368(1626):20120503.
    • (2013) Philos Trans R Soc Lond B Biol Sci , vol.368 , Issue.1626 , pp. 20120503
    • Lee, A.1    Nolan, A.2    Watson, J.3    Tristem, M.4
  • 7
    • 58149507192 scopus 로고    scopus 로고
    • Effects of retroviruses on host genome function
    • Jern P, Coffin JM (2008) Effects of retroviruses on host genome function. Annu Rev Genet 42:709-732.
    • (2008) Annu Rev Genet , vol.42 , pp. 709-732
    • Jern, P.1    Coffin, J.M.2
  • 8
    • 84861188188 scopus 로고    scopus 로고
    • Studies of endogenous retroviruses reveal a continuing evolutionary saga
    • Stoye JP (2012) Studies of endogenous retroviruses reveal a continuing evolutionary saga. Nat Rev Microbiol 10(6):395-406.
    • (2012) Nat Rev Microbiol , vol.10 , Issue.6 , pp. 395-406
    • Stoye, J.P.1
  • 9
    • 0042371625 scopus 로고    scopus 로고
    • The evolution, distribution and diversity of endogenous retroviruses
    • Gifford R, Tristem M (2003) The evolution, distribution and diversity of endogenous retroviruses. Virus Genes 26(3):291-315.
    • (2003) Virus Genes , vol.26 , Issue.3 , pp. 291-315
    • Gifford, R.1    Tristem, M.2
  • 10
    • 34548590461 scopus 로고    scopus 로고
    • Automated recognition of retroviral sequences in genomic data-RetroTector
    • Sperber GO, Airola T, Jern P, Blomberg J (2007) Automated recognition of retroviral sequences in genomic data-RetroTector. Nucleic Acids Res 35(15):4964-4976.
    • (2007) Nucleic Acids Res , vol.35 , Issue.15 , pp. 4964-4976
    • Sperber, G.O.1    Airola, T.2    Jern, P.3    Blomberg, J.4
  • 11
    • 84890276747 scopus 로고    scopus 로고
    • Broad-scale phylogenomics provides insights into retrovirus-host evolution
    • Hayward A, Grabherr M, Jern P (2013) Broad-scale phylogenomics provides insights into retrovirus-host evolution. Proc Natl Acad Sci USA 110(50):20146-20151.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.50 , pp. 20146-20151
    • Hayward, A.1    Grabherr, M.2    Jern, P.3
  • 12
    • 27344432183 scopus 로고    scopus 로고
    • Use of endogenous retroviral sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy
    • Jern P, Sperber GO, Blomberg J (2005) Use of endogenous retroviral sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy. Retrovirology 2:50.
    • (2005) Retrovirology , vol.2 , pp. 50
    • Jern, P.1    Sperber, G.O.2    Blomberg, J.3
  • 13
    • 84875692135 scopus 로고    scopus 로고
    • Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution
    • Smith JJ, et al. (2013) Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet 45(4):415-421.
    • (2013) Nat Genet , vol.45 , Issue.4 , pp. 415-421
    • Smith, J.J.1
  • 16
    • 58149500187 scopus 로고    scopus 로고
    • A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution
    • Gifford RJ, et al. (2008) A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution. Proc Natl Acad Sci USA 105(51):20362-20367.
    • (2008) Proc Natl Acad Sci USA , vol.105 , Issue.51 , pp. 20362-20367
    • Gifford, R.J.1
  • 17
    • 63449127325 scopus 로고    scopus 로고
    • Parallel germline infiltration of a lentivirus in two Malagasy lemurs
    • Gilbert C, Maxfield DG, Goodman SM, Feschotte C (2009) Parallel germline infiltration of a lentivirus in two Malagasy lemurs. PLoS Genet 5(3):e1000425.
    • (2009) PLoS Genet , vol.5 , Issue.3 , pp. e1000425
    • Gilbert, C.1    Maxfield, D.G.2    Goodman, S.M.3    Feschotte, C.4
  • 18
    • 0033049550 scopus 로고    scopus 로고
    • Interclass transmission and phyletic host tracking in murine leukemia virus-related retroviruses
    • Martin J, Herniou E, Cook J, O'Neill RW, Tristem M (1999) Interclass transmission and phyletic host tracking in murine leukemia virus-related retroviruses. J Virol 73(3): 2442-2449.
    • (1999) J Virol , vol.73 , Issue.3 , pp. 2442-2449
    • Martin, J.1    Herniou, E.2    Cook, J.3    O'neill, R.W.4    Tristem, M.5
  • 20
    • 84874065243 scopus 로고    scopus 로고
    • Beyond insecticides: New thinking on an ancient problem
    • McGraw EA, O'Neill SL (2013) Beyond insecticides: New thinking on an ancient problem. Nat Rev Microbiol 11(3):181-193.
    • (2013) Nat Rev Microbiol , vol.11 , Issue.3 , pp. 181-193
    • McGraw, E.A.1    O'neill, S.L.2
  • 21
    • 77951778552 scopus 로고    scopus 로고
    • A role for hostparasite interactions in the horizontal transfer of transposons across phyla
    • Gilbert C, Schaack S, Pace JK, 2nd, Brindley PJ, Feschotte C (2010) A role for hostparasite interactions in the horizontal transfer of transposons across phyla. Nature 464(7293):1347-1350.
    • (2010) Nature , vol.464 , Issue.7293 , pp. 1347-1350
    • Gilbert, C.1    Schaack, S.2    Pace, J.K.3    Brindley, P.J.4    Feschotte, C.5
  • 22
    • 78650169956 scopus 로고    scopus 로고
    • The impact of conservation on the status of the world's vertebrates
    • Hoffmann M, et al. (2010) The impact of conservation on the status of the world's vertebrates. Science 330(6010):1503-1509.
    • (2010) Science , vol.330 , Issue.6010 , pp. 1503-1509
    • Hoffmann, M.1
  • 23
    • 84869003221 scopus 로고    scopus 로고
    • Analyses of pig genomes provide insight into porcine demography and evolution
    • Groenen MA, et al. (2012) Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491(7424):393-398.
    • (2012) Nature , vol.491 , Issue.7424 , pp. 393-398
    • Groenen, M.A.1
  • 25
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis A (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22(21):2688-2690.
    • (2006) Bioinformatics , vol.22 , Issue.21 , pp. 2688-2690
    • Stamatakis, A.1
  • 27
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2-approximately maximum-likelihood trees for large alignments
    • Price MN, Dehal PS, Arkin AP (2010) FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 5(3):e9490.
    • (2010) PLoS ONE , vol.5 , Issue.3 , pp. e9490
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 28
    • 80055070300 scopus 로고    scopus 로고
    • Impacts of the Cretaceous terrestrial revolution and KPg extinction on mammal diversification
    • Meredith RW, et al. (2011) Impacts of the Cretaceous terrestrial revolution and KPg extinction on mammal diversification. Science 334(6055):521-524.
    • (2011) Science , vol.334 , Issue.6055 , pp. 521-524
    • Meredith, R.W.1
  • 29
    • 34047108602 scopus 로고    scopus 로고
    • The delayed rise of present-day mammals
    • Bininda-Emonds OR, et al. (2007) The delayed rise of present-day mammals. Nature 446(7135):507-512.
    • (2007) Nature , vol.446 , Issue.7135 , pp. 507-512
    • Bininda-Emonds, O.R.1
  • 30
    • 84869088692 scopus 로고    scopus 로고
    • The global diversity of birds in space and time
    • Jetz W, Thomas GH, Joy JB, Hartmann K, Mooers AO (2012) The global diversity of birds in space and time. Nature 491(7424):444-448.
    • (2012) Nature , vol.491 , Issue.7424 , pp. 444-448
    • Jetz, W.1    Thomas, G.H.2    Joy, J.B.3    Hartmann, K.4    Mooers, A.O.5
  • 31
    • 84876271982 scopus 로고    scopus 로고
    • The African coelacanth genome provides insights into tetrapod evolution
    • Amemiya CT, et al. (2013) The African coelacanth genome provides insights into tetrapod evolution. Nature 496(7445):311-316.
    • (2013) Nature , vol.496 , Issue.7445 , pp. 311-316
    • Amemiya, C.T.1
  • 32
    • 84879020737 scopus 로고    scopus 로고
    • The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage
    • Shaffer HB, et al. (2013) The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biol 14(3):R28.
    • (2013) Genome Biol , vol.14 , Issue.3 , pp. R28
    • Shaffer, H.B.1
  • 33
    • 77749279661 scopus 로고    scopus 로고
    • General quantitative genetic methods for comparative biology: Phylogenies, taxonomies and multi-trait models for continuous and categorical characters
    • Hadfield JD, Nakagawa S (2010) General quantitative genetic methods for comparative biology: Phylogenies, taxonomies and multi-trait models for continuous and categorical characters. J Evol Biol 23(3):494-508.
    • (2010) J Evol Biol , vol.23 , Issue.3 , pp. 494-508
    • Hadfield, J.D.1    Nakagawa, S.2
  • 34
    • 77749249761 scopus 로고    scopus 로고
    • MCMC methods for multi-response generalised linear mixed models: The MCMCglmm R package
    • Hadfield J (2010) MCMC methods for multi-response generalised linear mixed models: The MCMCglmm R package. J Stat Softw 33(2):1-22.
    • (2010) J Stat Softw , vol.33 , Issue.2 , pp. 1-22
    • Hadfield, J.1
  • 35
    • 77956069051 scopus 로고    scopus 로고
    • Simple means to improve the interpretability of regression coefficients
    • Scheielzeth H (2010) Simple means to improve the interpretability of regression coefficients. Methods in Ecology and Evolution 1(2):103-113.
    • (2010) Methods in Ecology and Evolution , vol.1 , Issue.2 , pp. 103-113
    • Scheielzeth, H.1
  • 37
    • 41149087694 scopus 로고    scopus 로고
    • Convergence diagnosis and output analysis for MCMC
    • Plummer M, Best N, Cowles K, Vines K (2006) Convergence diagnosis and output analysis for MCMC. R News 6(1):7-11.
    • (2006) R News , vol.6 , Issue.1 , pp. 7-11
    • Plummer, M.1    Best, N.2    Cowles, K.3    Vines, K.4
  • 39
    • 84972492387 scopus 로고
    • Inference from iterative simulation using multiple sequences
    • Gelman A, Rubin D (1992) Inference from iterative simulation using multiple sequences. Stat Sci 7(4):457-511.
    • (1992) Stat Sci , vol.7 , Issue.4 , pp. 457-511
    • Gelman, A.1    Rubin, D.2
  • 40
    • 0001032163 scopus 로고
    • Evaluating the accuracy of sampling-based approaches to calculating posterior moments
    • eds Bernardo J, Berger J, Dawid A, Smith A (Clarendon, New York)
    • Geweke J (1992) Evaluating the accuracy of sampling-based approaches to calculating posterior moments. Bayesian Statistics, eds Bernardo J, Berger J, Dawid A, Smith A (Clarendon, New York).
    • (1992) Bayesian Statistics
    • Geweke, J.1
  • 41
    • 0024975994 scopus 로고
    • The phylogenetic regression
    • Grafen A (1989) The phylogenetic regression. Philos Trans R Soc Lond B Biol Sci 326(1233):119-157.
    • (1989) Philos Trans R Soc Lond B Biol Sci , vol.326 , Issue.1233 , pp. 119-157
    • Grafen, A.1
  • 42
    • 0036135468 scopus 로고    scopus 로고
    • Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach
    • Sanderson MJ (2002) Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach. Mol Biol Evol 19(1):101-109.
    • (2002) Mol Biol Evol , vol.19 , Issue.1 , pp. 101-109
    • Sanderson, M.J.1
  • 43
    • 1042304216 scopus 로고    scopus 로고
    • APE: Analyses of phylogenetics and evolution in R language
    • Paradis E, Claude J, Strimmer K (2004) APE: Analyses of phylogenetics and evolution in R language. Bioinformatics 20(2):289-290.
    • (2004) Bioinformatics , vol.20 , Issue.2 , pp. 289-290
    • Paradis, E.1    Claude, J.2    Strimmer, K.3


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