메뉴 건너뛰기




Volumn 6, Issue 2, 2014, Pages 416-432

A new genome-wide method to track horizontally transferred sequences: Application to Drosophila

Author keywords

Drosophila; FDR; Genome wide method; Horizontal transfer; Transposable elements

Indexed keywords

TRANSPOSON;

EID: 84902973300     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evu026     Document Type: Article
Times cited : (9)

References (97)
  • 3
    • 21144441817 scopus 로고    scopus 로고
    • Lateral gene transfer in eukaryotes
    • Andersson JO. 2005. Lateral gene transfer in eukaryotes. Cell Mol Life Sci. 62: 1182-1197.
    • (2005) Cell Mol Life Sci , vol.62 , pp. 1182-1197
    • Andersson, J.O.1
  • 4
    • 0024009771 scopus 로고
    • Molecular characteristics of diverse populations are consistent with the hypothesis of a recent invasion of Drosophila melanogaster by mobile P elements
    • Anxolabéhère D, Kidwell MG, Periquet G. 1988. Molecular characteristics of diverse populations are consistent with the hypothesis of a recent invasion of Drosophila melanogaster by mobile P elements. Mol Biol Evol. 5: 252-269.
    • (1988) Mol Biol Evol , vol.5 , pp. 252-269
    • Anxolabéhère, D.1    Kidwell, M.G.2    Periquet, G.3
  • 6
    • 79956022978 scopus 로고    scopus 로고
    • Towardsmore robustmethods of alien gene detection
    • Azad RK, Lawrence JG. 2011. Towardsmore robustmethods of alien gene detection. Nucleic Acids Res. 39:e56.
    • (2011) Nucleic Acids Res , vol.39
    • Azad, R.K.1    Lawrence, J.G.2
  • 7
    • 78751652118 scopus 로고    scopus 로고
    • Ninety years of Drosophila melanogaster hybrids
    • Barbash DA. 2010. Ninety years of Drosophila melanogaster hybrids. Genetics 186: 1-8.
    • (2010) Genetics , vol.186 , pp. 1-8
    • Barbash, D.A.1
  • 8
    • 62349104354 scopus 로고    scopus 로고
    • Widespread evidence for horizontal transfer of transposable elements across Drosophila genomes
    • Bartolomé C, Bello X,Maside X. 2009. Widespread evidence for horizontal transfer of transposable elements across Drosophila genomes. Genome Biol. 10:R22.
    • (2009) Genome Biol , vol.10
    • Bartolomé, C.1    Bello Xmaside, X.2
  • 9
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Statist Soc. 57: 289-300.
    • (1995) J Roy Statist Soc , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 10
    • 0004049988 scopus 로고    scopus 로고
    • The control of the false discovery rate in multiple testing under dependency
    • Benjamini Y, Yekutieli D. 2001. The control of the false discovery rate in multiple testing under dependency. Ann Statist. 10: 467-498.
    • (2001) Ann Statist , vol.10 , pp. 467-498
    • Benjamini, Y.1    Yekutieli, D.2
  • 11
    • 0034828182 scopus 로고    scopus 로고
    • Drosophila euchromatic LTR retrotransposons are much younger than the host species in which they reside
    • Bowen NJ, McDonald JF. 2001. Drosophila euchromatic LTR retrotransposons are much younger than the host species in which they reside. Genome Res. 11: 1527-1540.
    • (2001) Genome Res , vol.11 , pp. 1527-1540
    • Bowen, N.J.1    McDonald, J.F.2
  • 12
    • 84883225153 scopus 로고    scopus 로고
    • A selective sweep across species boundaries in Drosophila
    • Brand CL, Kingan SB, Wu L, Garrigan D. 2013. A selective sweep across species boundaries in Drosophila. Mol Biol Evol. 30: 2177-2186.
    • (2013) Mol Biol Evol , vol.30 , pp. 2177-2186
    • Brand, C.L.1    Kingan, S.B.2    Wu, L.3    Garrigan, D.4
  • 13
    • 0028058068 scopus 로고
    • The strange phylogenies of transposable elements: Are horizontal transfers the only explanation?
    • Capy P, Anxolabéhère D, Langin T. 1994. The strange phylogenies of transposable elements: are horizontal transfers the only explanation? Trends Genet. 10: 7-12.
    • (1994) Trends Genet , vol.10 , pp. 7-12
    • Capy, P.1    Anxolabéhère, D.2    Langin, T.3
  • 14
    • 84863686948 scopus 로고    scopus 로고
    • Tropical Africa as a cradle for horizontal transfers of transposable elements between species of the genera Drosophila and Zaprionus
    • Carareto CM. 2011. Tropical Africa as a cradle for horizontal transfers of transposable elements between species of the genera Drosophila and Zaprionus. Mob Genet Elem. 1: 179-186.
    • (2011) Mob Genet Elem , vol.1 , pp. 179-186
    • Carareto, C.M.1
  • 15
    • 35348873167 scopus 로고    scopus 로고
    • Purifying selection maintains highly conserved noncoding sequences in Drosophila
    • Casillas S, Barbadilla A, Bergman CM. 2007. Purifying selection maintains highly conserved noncoding sequences in Drosophila. Mol Biol Evol. 24: 2222-2234.
    • (2007) Mol Biol Evol , vol.24 , pp. 2222-2234
    • Casillas, S.1    Barbadilla, A.2    Bergman, C.M.3
  • 16
    • 0025093426 scopus 로고
    • Evidence for horizontal transmission of the P transposable element between Drosophila species
    • Daniels SB, et al. 1990. Evidence for horizontal transmission of the P transposable element between Drosophila species. Genetics 124: 339-355.
    • (1990) Genetics , vol.124 , pp. 339-355
    • Daniels, S.B.1
  • 17
    • 84872458470 scopus 로고    scopus 로고
    • Methods for detection of horizontal transfer of transposable elements in complete genomes
    • de Carvalho MO, Loreto ELS. 2012. Methods for detection of horizontal transfer of transposable elements in complete genomes. Genet Mol Biol. 35: 1078-1084.
    • (2012) Genet Mol Biol , vol.35 , pp. 1078-1084
    • De Carvalho, M.O.1    Loreto, E.L.S.2
  • 18
    • 84855281420 scopus 로고    scopus 로고
    • Repetitive elements may comprise over twothirds of the human genome
    • de Koning AP, et al. 2011. Repetitive elements may comprise over twothirds of the human genome. PLoS Genet. 7:e1002384.
    • (2011) PLoS Genet , vol.7
    • De Koning, A.P.1
  • 19
    • 69549126582 scopus 로고    scopus 로고
    • Evolutionary dynamics of the LTR retrotransposons roo and rooA inferred from twelve complete Drosophila genomes
    • de la Chaux N, Wagner A. 2009. Evolutionary dynamics of the LTR retrotransposons roo and rooA inferred from twelve complete Drosophila genomes. BMC Evol Biol. 9: 205.
    • (2009) BMC Evol Biol , vol.9 , pp. 205
    • De La Chaux, N.1    Wagner, A.2
  • 20
    • 84869026655 scopus 로고    scopus 로고
    • Ancestral polymorphism and recent invasion of transposable elements in Drosophila species
    • Dias ES, Carareto CMA. 2012. Ancestral polymorphism and recent invasion of transposable elements in Drosophila species. BMC Evol Biol. 12: 119.
    • (2012) BMC Evol Biol , vol.12 , pp. 119
    • Dias, E.S.1    Carareto, C.M.A.2
  • 21
    • 0020172456 scopus 로고
    • Differing levels of dispersed repetitive DNA among closely related species of Drosophila
    • Dowsett AE, Young MW. 1982. Differing levels of dispersed repetitive DNA among closely related species of Drosophila. Proc Natl Acad Sci U S A. 79: 4570-4574.
    • (1982) Proc Natl Acad Sci U S A. , vol.79 , pp. 4570-4574
    • Dowsett, A.E.1    Young, M.W.2
  • 22
    • 80053210637 scopus 로고    scopus 로고
    • Models, algorithms and programs for phylogeny reconciliation
    • Doyon JP, Ranwez V, Daubin V, Berry V. 2011. Models, algorithms and programs for phylogeny reconciliation. Brief Bioinform. 12: 392-400.
    • (2011) Brief Bioinform , vol.12 , pp. 392-400
    • Doyon, J.P.1    Ranwez, V.2    Daubin, V.3    Berry, V.4
  • 23
    • 47149117454 scopus 로고    scopus 로고
    • Evolution of genes and genomes on the Drosophila phylogeny
    • Drosophila 12 Genomes Consortium
    • Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.
    • (2007) Nature , vol.450 , pp. 203-218
  • 24
    • 79955140811 scopus 로고    scopus 로고
    • Transfer of a chromosomalMaverick to endogenous bracovirus in a parasitoid wasp
    • Dupuy C, et al. 2011. Transfer of a chromosomalMaverick to endogenous bracovirus in a parasitoid wasp. Genetica 139: 489-496.
    • (2011) Genetica , vol.139 , pp. 489-496
    • Dupuy, C.1
  • 26
    • 42349100413 scopus 로고    scopus 로고
    • Horizontal gene transfer regulation in bacteria as a "spandrel" of DNA repair mechanisms
    • Fall S, et al. 2007. Horizontal gene transfer regulation in bacteria as a "spandrel" of DNA repair mechanisms. PLoS One 2:e1055.
    • (2007) PLoS One , vol.2
    • Fall, S.1
  • 27
    • 0031127307 scopus 로고    scopus 로고
    • Transposable elements: How non-LTR retrotransposons do it
    • Finnegan DJ. 1997. Transposable elements: how non-LTR retrotransposons do it. Curr Biol. 7:R245-R248. (Pubitemid 27176843)
    • (1997) Current Biology , vol.7 , Issue.4
    • Finnegan, D.J.1
  • 28
    • 0036108220 scopus 로고    scopus 로고
    • Multiple hypotheses testing and expected number of type i errors
    • Finner H, Roters M. 2002. Multiple hypotheses testing and expected number of type I. errors. Ann Statist. 30: 220-238.
    • (2002) Ann Statist , vol.30 , pp. 220-238
    • Finner, H.1    Roters, M.2
  • 29
    • 84859992850 scopus 로고    scopus 로고
    • What makes transposable elements move in the Drosophila genome?
    • García Guerreiro MP. 2012. What makes transposable elements move in the Drosophila genome? Heredity 108: 461-468.
    • (2012) Heredity , vol.108 , pp. 461-468
    • García Guerreiro, M.P.1
  • 30
    • 84868117105 scopus 로고    scopus 로고
    • Quantifying introgression risk with realistic population genetics
    • Ghosh A, Meirmans PG, Haccou P. 2012. Quantifying introgression risk with realistic population genetics. Proc Biol Sci. 279: 4747-4754.
    • (2012) Proc Biol Sci , vol.279 , pp. 4747-4754
    • Ghosh, A.1    Meirmans, P.G.2    Haccou, P.3
  • 31
    • 84885955856 scopus 로고    scopus 로고
    • Horizontal transfer and evolution of prokaryote transposable elements in eukaryotes
    • Gilbert C, Cordaux R. 2013. Horizontal transfer and evolution of prokaryote transposable elements in eukaryotes. Genome Biol Evol. 5: 822-832.
    • (2013) Genome Biol Evol , vol.5 , pp. 822-832
    • Gilbert, C.1    Cordaux, R.2
  • 33
    • 84874269744 scopus 로고    scopus 로고
    • Horizontal transfer of OC1 transposons in the Tasmanian devil
    • Gilbert C, Waters P, Feschotte C, Schaack S. 2013. Horizontal transfer of OC1 transposons in the Tasmanian devil. BMC Genomics 14: 134.
    • (2013) BMC Genomics , vol.14 , pp. 134
    • Gilbert, C.1    Waters, P.2    Feschotte, C.3    Schaack, S.4
  • 34
    • 77951778552 scopus 로고    scopus 로고
    • A role for host-parasite interactions in the horizontal transfer of transposons across phyla
    • Gilbert C, et al. 2010. A role for host-parasite interactions in the horizontal transfer of transposons across phyla. Nature 464: 1347-1350.
    • (2010) Nature , vol.464 , pp. 1347-1350
    • Gilbert, C.1
  • 35
    • 80955180036 scopus 로고    scopus 로고
    • Vertical inheritance and bursts of transposition have shaped the evolution of the BS non- LTR retrotransposon in Drosophila
    • Granzotto A, Lopes FR, Vieira C, Carareto CMA. 2011. Vertical inheritance and bursts of transposition have shaped the evolution of the BS non- LTR retrotransposon in Drosophila. Mol Genet Genomics. 286: 57-66.
    • (2011) Mol Genet Genomics , vol.286 , pp. 57-66
    • Granzotto, A.1    Lopes, F.R.2    Vieira, C.3    Carareto, C.M.A.4
  • 36
    • 84876561639 scopus 로고    scopus 로고
    • Inference of natural selection from interspersed genomic elements based on polymorphism and divergence
    • Gronau I, Arbiza L, Mohammed J, Siepel A. 2013. Inference of natural selection from interspersed genomic elements based on polymorphism and divergence. Mol Biol Evol. 30: 1159-1171.
    • (2013) Mol Biol Evol , vol.30 , pp. 1159-1171
    • Gronau, I.1    Arbiza, L.2    Mohammed, J.3    Siepel, A.4
  • 37
    • 38549148421 scopus 로고    scopus 로고
    • Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes
    • Heger A, Ponting CP. 2007. Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes. Genome Res. 17: 1837-1849.
    • (2007) Genome Res , vol.17 , pp. 1837-1849
    • Heger, A.1    Ponting, C.P.2
  • 38
    • 84871958299 scopus 로고    scopus 로고
    • A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence
    • Hu TT, Eisen MB, Thornton KR, Andolfatto P. 2013. A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence. Genome Res. 23: 89-98.
    • (2013) Genome Res , vol.23 , pp. 89-98
    • Hu, T.T.1    Eisen, M.B.2    Thornton, K.R.3    Andolfatto, P.4
  • 39
    • 79551634894 scopus 로고    scopus 로고
    • PHAST and RPHAST: Phylogenetic analysis with space/time models
    • Hubisz MJ, Pollard KS, Siepel A. 2011. PHAST and RPHAST: phylogenetic analysis with space/time models. Brief Bioinform. 12: 41-51.
    • (2011) Brief Bioinform , vol.12 , pp. 41-51
    • Hubisz, M.J.1    Pollard, K.S.2    Siepel, A.3
  • 40
    • 60149088444 scopus 로고    scopus 로고
    • Genomic islands: Tools of bacterial horizontal gene transfer and evolution
    • Juhas M, et al. 2009. Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol Rev. 33: 376-393.
    • (2009) FEMS Microbiol Rev , vol.33 , pp. 376-393
    • Juhas, M.1
  • 41
    • 80052854314 scopus 로고    scopus 로고
    • Families of transposable elements, population structure and the origin of species
    • Jurka J, Bao W, Kojima KK. 2011. Families of transposable elements, population structure and the origin of species. Biol Direct. 6: 44.
    • (2011) Biol Direct , vol.6 , pp. 44
    • Jurka, J.1    Bao, W.2    Kojima, K.K.3
  • 42
    • 84867748191 scopus 로고    scopus 로고
    • Distinct groups of repetitive families preserved in mammals correspond to different periods of regulatory innovations in vertebrates
    • Jurka J, et al. 2012. Distinct groups of repetitive families preserved in mammals correspond to different periods of regulatory innovations in vertebrates. Biol Direct. 7: 36.
    • (2012) Biol Direct , vol.7 , pp. 36
    • Jurka, J.1
  • 43
    • 0012341115 scopus 로고    scopus 로고
    • The transposable elements of the Drosophila melanogaster euchromatin: A genomics perspective
    • Kaminker JS, et al. 2002. The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol. 3: RESEARCH0084.
    • (2002) Genome Biol , vol.3
    • Kaminker, J.S.1
  • 44
    • 0037975554 scopus 로고    scopus 로고
    • Molecular paleontology of transposable elements in the Drosophila melanogaster genome
    • Kapitonov VV, Jurka J. 2003. Molecular paleontology of transposable elements in the Drosophila melanogaster genome. Proc Natl Acad Sci U S A. 100: 6569-74.
    • (2003) Proc Natl Acad Sci U S A. , vol.100 , pp. 6569-6574
    • Kapitonov, V.V.1    Jurka, J.2
  • 45
    • 47649104484 scopus 로고    scopus 로고
    • Horizontal gene transfer in eukaryotic evolution
    • Keeling PJ, Palmer JD. 2008. Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet. 9: 605-618.
    • (2008) Nat Rev Genet , vol.9 , pp. 605-618
    • Keeling, P.J.1    Palmer, J.D.2
  • 46
    • 0028351915 scopus 로고
    • Rodent BC1 RNA gene as a master gene for ID element amplification
    • Kim J, et al. 1994. Rodent BC1 RNA gene as a master gene for ID element amplification. Proc Natl Acad Sci U S A. 91: 3607-3611.
    • (1994) Proc Natl Acad Sci U S A. , vol.91 , pp. 3607-3611
    • Kim, J.1
  • 47
    • 84857498958 scopus 로고    scopus 로고
    • Sequencing of pooled DNA samples (Pool-Seq) uncovers complex dynamics of transposable element insertions in Drosophilamelanogaster
    • Kofler R, Betancourt AJ, Schlötterer C, Schlo C. 2012. Sequencing of pooled DNA samples (Pool-Seq) uncovers complex dynamics of transposable element insertions in Drosophilamelanogaster. PLoSGenet. 8: e1002487.
    • (2012) PLoSGenet , vol.8
    • Kofler, R.1    Betancourt, A.J.2    Schlötterer, C.3    Schlo, C.4
  • 48
    • 84866744388 scopus 로고    scopus 로고
    • Integrating prior knowledge in multiple testing under dependence with applications to detecting differential DNA methylation
    • Kuan PF, Chiang DY. 2012. Integrating prior knowledge in multiple testing under dependence with applications to detecting differential DNA methylation. Biometrics 68: 774-783.
    • (2012) Biometrics , vol.68 , pp. 774-783
    • Kuan, P.F.1    Chiang, D.Y.2
  • 49
    • 0000792280 scopus 로고
    • Historical biogeography of the Drosophila melanogaster species subgroup
    • Hecht MK, Wallace B, Prance GT, editors Springer
    • Lachaise D, et al. 1988. Historical biogeography of the Drosophila melanogaster species subgroup. In: Hecht MK, Wallace B, Prance GT, editors. Evolutionary biology. Springer. p. 159-225.
    • (1988) Evolutionary Biology , pp. 159-225
    • Lachaise, D.1
  • 50
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • Lander ES, et al. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
    • (2001) Nature , vol.409 , pp. 860-921
    • Lander, E.S.1
  • 51
    • 15544374910 scopus 로고    scopus 로고
    • The first steps of transposable elements invasion: Parasitic strategy vs genetic drift
    • Le Rouzic A, Capy P. 2005. The first steps of transposable elements invasion: parasitic strategy vs. genetic drift. Genetics 169: 1033-1043.
    • (2005) Genetics , vol.169 , pp. 1033-1043
    • Le Rouzic, A.1    Capy, P.2
  • 52
    • 84876563936 scopus 로고    scopus 로고
    • Reconstructing the evolutionary history of transposable elements
    • Le Rouzic A, Payen T, Hua-Van A. 2013. Reconstructing the evolutionary history of transposable elements. Genome Biol Evol. 5: 77-86.
    • (2013) Genome Biol Evol , vol.5 , pp. 77-86
    • Le Rouzic, A.1    Payen, T.2    Hua-Van, A.3
  • 53
    • 79551681942 scopus 로고    scopus 로고
    • Comparative analysis of transposable elements in the melanogaster subgroup sequenced genomes
    • Lerat E, Burlet N, Biémont C, Vieira C. 2011. Comparative analysis of transposable elements in the melanogaster subgroup sequenced genomes. Gene 473: 100-109.
    • (2011) Gene , vol.473 , pp. 100-109
    • Lerat, E.1    Burlet, N.2    Biémont, C.3    Vieira, C.4
  • 54
    • 0042525765 scopus 로고    scopus 로고
    • Sequence divergence within transposable element families in the Drosophila melanogaster genome
    • Lerat E, Rizzon C, Biémont C. 2003. Sequence divergence within transposable element families in the Drosophila melanogaster genome. Genome Res. 13: 1889-1896.
    • (2003) Genome Res , vol.13 , pp. 1889-1896
    • Lerat, E.1    Rizzon, C.2    Biémont, C.3
  • 55
    • 55949115391 scopus 로고    scopus 로고
    • A new SPIN on horizontal transfer
    • Lisch D. 2008. A new SPIN on horizontal transfer. Proc Natl Acad Sci U S A. 105: 16827-16828.
    • (2008) Proc Natl Acad Sci U S A. , vol.105 , pp. 16827-16828
    • Lisch, D.1
  • 56
    • 44349148619 scopus 로고    scopus 로고
    • Revisiting horizontal transfer of transposable elements in Drosophila
    • Loreto ELS, Carareto CMA, Capy P. 2008. Revisiting horizontal transfer of transposable elements in Drosophila. Heredity 100: 545-554.
    • (2008) Heredity , vol.100 , pp. 545-554
    • Loreto, E.L.S.1    Carareto, C.M.A.2    Capy, P.3
  • 57
    • 40849120757 scopus 로고    scopus 로고
    • Multiple invasions of Errantivirus in the genus Drosophila
    • Ludwig A, Valente VL, Loreto EL. 2008.Multiple invasions of Errantivirus in the genus Drosophila. Insect Mol Biol. 17: 113-124.
    • (2008) Insect Mol Biol , vol.17 , pp. 113-124
    • Ludwig, A.1    Valente, V.L.2    Loreto, E.L.3
  • 58
    • 34547396004 scopus 로고    scopus 로고
    • The frailty of adaptive hypotheses for the origins of organismal complexity
    • Lynch M. 2007. The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci U S A. 104: 8597-8604.
    • (2007) Proc Natl Acad Sci U S A. , vol.104 , pp. 8597-8604
    • Lynch, M.1
  • 59
    • 10744222156 scopus 로고    scopus 로고
    • Identification and characterization of multi-species conserved sequences
    • Margulies EH, Blanchette M, Haussler D, Green ED. 2003. Identification and characterization of multi-species conserved sequences. Genome Res. 13: 2507-2518.
    • (2003) Genome Res , vol.13 , pp. 2507-2518
    • Margulies, E.H.1    Blanchette, M.2    Haussler, D.3    Green, E.D.4
  • 60
    • 84876556121 scopus 로고    scopus 로고
    • Flybase: Improvements to the bibliography
    • Marygold SJ, et al. 2013. Flybase: improvements to the bibliography. Nucleic Acids Res. 41: 751-757.
    • (2013) Nucleic Acids Res , vol.41 , pp. 751-757
    • Marygold, S.J.1
  • 61
    • 1642357230 scopus 로고    scopus 로고
    • Molecular polymorphism in Drosophila melanogaster and d simulans: What have we learned from recent studies?
    • Mousset S, Derome N. 2004. Molecular polymorphism in Drosophila melanogaster and d. simulans: what have we learned from recent studies? Genetica 120: 79-86.
    • (2004) Genetica , vol.120 , pp. 79-86
    • Mousset, S.1    Derome, N.2
  • 62
    • 70350515004 scopus 로고    scopus 로고
    • Unexpected consequences of a sudden and massive transposon amplification on rice gene expression
    • Naito K, et al. 2009. Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature 461: 1130-1134.
    • (2009) Nature , vol.461 , pp. 1130-1134
    • Naito, K.1
  • 63
    • 40849127131 scopus 로고    scopus 로고
    • African Drosophila melanogaster and D simulans populations have similar levels of sequence variability, suggesting comparable effective population sizes
    • Nolte V, Schlötterer C. 2008. African Drosophila melanogaster and D. simulans populations have similar levels of sequence variability, suggesting comparable effective population sizes. Genetics 178: 405-412.
    • (2008) Genetics , vol.178 , pp. 405-412
    • Nolte, V.1    Schlötterer, C.2
  • 64
    • 77954854627 scopus 로고    scopus 로고
    • Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data
    • Novãk E, Neumann P, Macas J. 2010. Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinformatics 11: 378.
    • (2010) BMC Bioinformatics , vol.11 , pp. 378
    • Novãk, E.1    Neumann, P.2    MacAs, J.3
  • 65
    • 74049139612 scopus 로고    scopus 로고
    • Transpositionally active episomal hAT elements
    • O'Brochta DA, et al. 2009. Transpositionally active episomal hAT elements. BMC Mol Biol. 10: 108.
    • (2009) BMC Mol Biol , vol.10 , pp. 108
    • O'Brochta, D.A.1
  • 66
    • 0034682335 scopus 로고    scopus 로고
    • Lateral gene transfer and the nature of bacterial innovation
    • Ochman H, Lawrence JG, Groisman EA. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299-304.
    • (2000) Nature , vol.405 , pp. 299-304
    • Ochman, H.1    Lawrence, J.G.2    Groisman, E.A.3
  • 67
    • 34147105638 scopus 로고    scopus 로고
    • The evolutionary history of human DNA transposons: Evidence for intense activity in the primate lineage
    • Pace JK, Feschotte C. 2007. The evolutionary history of human DNA transposons: evidence for intense activity in the primate lineage. Genome Res. 17: 422-432.
    • (2007) Genome Res , vol.17 , pp. 422-432
    • Pace, J.K.1    Feschotte, C.2
  • 68
    • 55949134735 scopus 로고    scopus 로고
    • Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods
    • Pace JK, Gilbert C, Clark MS, Feschotte C. 2008. Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods. Proc Natl Acad Sci U S A. 105: 17023-17028.
    • (2008) Proc Natl Acad Sci U S A. , vol.105 , pp. 17023-17028
    • Pace, J.K.1    Gilbert, C.2    Clark, M.S.3    Feschotte, C.4
  • 69
    • 0034914597 scopus 로고    scopus 로고
    • The evolutionary life history of P transposons: From horizontal invaders to domesticated neogenes
    • Pinsker W, Haring E, Hagemann S, Miller WJ. 2001. The evolutionary life history of P transposons: from horizontal invaders to domesticated neogenes. Chromosoma 110: 148-158.
    • (2001) Chromosoma , vol.110 , pp. 148-158
    • Pinsker, W.1    Haring, E.2    Hagemann, S.3    Miller, W.J.4
  • 70
    • 34447513240 scopus 로고    scopus 로고
    • DarkHorse: A method for genome-wide prediction of horizontal gene transfer
    • Podell S, Gaasterland T. 2007. DarkHorse: a method for genome-wide prediction of horizontal gene transfer. Genome Biol. 8:R16.
    • (2007) Genome Biol , vol.8
    • Podell, S.1    Gaasterland, T.2
  • 71
    • 74949092081 scopus 로고    scopus 로고
    • Detection of nonneutral substitution rates on mammalian phylogenies
    • Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. 2010. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 20: 110-121.
    • (2010) Genome Res , vol.20 , pp. 110-121
    • Pollard, K.S.1    Hubisz, M.J.2    Rosenbloom, K.R.3    Siepel, A.4
  • 72
    • 33748778231 scopus 로고    scopus 로고
    • A computational tool for the genomic identification of regions of unusual compositional properties and its utilization in the detection of horizontally transferred sequences
    • Putonti C, et al. 2006. A computational tool for the genomic identification of regions of unusual compositional properties and its utilization in the detection of horizontally transferred sequences. Mol Biol Evol. 23: 1863-1868.
    • (2006) Mol Biol Evol , vol.23 , pp. 1863-1868
    • Putonti, C.1
  • 73
    • 77951770756 scopus 로고    scopus 로고
    • Bedtools: A flexible suite of utilities for comparing genomic features
    • Quinlan AR, Hall IM. 2010. Bedtools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 74
    • 84863304598 scopus 로고    scopus 로고
    • R Core Team Vienna (Austria): R Foundation for Statistical Computing
    • R Core Team. 2013. R: a language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing.
    • (2013) R: A Language and Environment for Statistical Computing
  • 75
    • 0035546223 scopus 로고    scopus 로고
    • Detection of lateral gene transfer among microbial genomes
    • Ragan MA. 2001. Detection of lateral gene transfer among microbial genomes. Curr Opin Genet Dev. 11: 620-626.
    • (2001) Curr Opin Genet Dev , vol.11 , pp. 620-626
    • Ragan, M.A.1
  • 76
    • 43149103661 scopus 로고    scopus 로고
    • Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus
    • Ray DA, et al. 2008. Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus. Genome Res. 18: 717-728.
    • (2008) Genome Res , vol.18 , pp. 717-728
    • Ray, D.A.1
  • 77
    • 0032702602 scopus 로고    scopus 로고
    • Reconstructing early events in eukaryotic evolution
    • Roger A. 1999. Reconstructing early events in eukaryotic evolution. Am Nat. 154:S146-S163.
    • (1999) Am Nat , vol.154
    • Roger, A.1
  • 78
    • 1642417203 scopus 로고    scopus 로고
    • Genetics of hybrid inviability and sterility in Drosophila: Dissection of introgression of D simulans genes in D melanogaster genome
    • Sawamura K, Karr TL, Yamamoto MT. 2004. Genetics of hybrid inviability and sterility in Drosophila: dissection of introgression of D. simulans genes in D. melanogaster genome. Genetica 120: 253-260.
    • (2004) Genetica , vol.120 , pp. 253-260
    • Sawamura, K.1    Karr, T.L.2    Yamamoto, M.T.3
  • 79
    • 77955658052 scopus 로고    scopus 로고
    • Promiscuous DNA: Horizontal transfer of transposable elements and why it matters for eukaryotic evolution
    • Schaack S, Gilbert C, Feschotte C. 2010. Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends Ecol Evol. 25: 537-546.
    • (2010) Trends Ecol Evol , vol.25 , pp. 537-546
    • Schaack, S.1    Gilbert, C.2    Feschotte, C.3
  • 80
    • 70450202132 scopus 로고    scopus 로고
    • The B73 maize genome: Complexity, diversity, and dynamics
    • Schnable PS, et al. 2009. The B73 maize genome: complexity, diversity, and dynamics. Science 326: 1112-1115.
    • (2009) Science , vol.326 , pp. 1112-1115
    • Schnable, P.S.1
  • 81
    • 27744551559 scopus 로고    scopus 로고
    • Identification and categorization of horizontally transferred genes in prokaryotic genomes
    • Shi SY, Cai XH, Ding DF. 2005. Identification and categorization of horizontally transferred genes in prokaryotic genomes. Acta Biochim Biophys Sin. 37: 561-566.
    • (2005) Acta Biochim Biophys Sin , vol.37 , pp. 561-566
    • Shi, S.Y.1    Cai, X.H.2    Ding, D.F.3
  • 82
    • 23744458086 scopus 로고    scopus 로고
    • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    • Siepel A, et al. 2005. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15: 1034-1050.
    • (2005) Genome Res , vol.15 , pp. 1034-1050
    • Siepel, A.1
  • 83
    • 0344876091 scopus 로고    scopus 로고
    • Factors that affect the horizontal transfer of transposable elements
    • Silva JC, Loreto EL, Clark JB. 2004. Factors that affect the horizontal transfer of transposable elements. Curr Issues Mol Biol. 6: 57-71.
    • (2004) Curr Issues Mol Biol , vol.6 , pp. 57-71
    • Silva, J.C.1    Loreto, E.L.2    Clark, J.B.3
  • 84
    • 33846589670 scopus 로고    scopus 로고
    • The recent demographic and adaptive history of Drosophila melanogaster
    • Stephan W, Li H. 2007. The recent demographic and adaptive history of Drosophila melanogaster. Heredity 98: 65-68.
    • (2007) Heredity , vol.98 , pp. 65-68
    • Stephan, W.1    Li, H.2
  • 85
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genomewide studies
    • Storey JD, Tibshirani R. 2003. Statistical significance for genomewide studies. Proc Natl Acad Sci U S A. 100: 9440-9445.
    • (2003) Proc Natl Acad Sci U S A. , vol.100 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2
  • 86
    • 62849107228 scopus 로고    scopus 로고
    • Large-scale multiple testing under dependence
    • Sun W, Tony Cai T. 2009. Large-scale multiple testing under dependence. J Roy Statist Soc. 71: 393-424.
    • (2009) J Roy Statist Soc , vol.71 , pp. 393-424
    • Sun, W.1    Tony Cai, T.2
  • 87
    • 1242352089 scopus 로고    scopus 로고
    • Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks
    • Tamura K, Subramanian S, Kumar S. 2004. Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol Biol Evol. 21: 36-44.
    • (2004) Mol Biol Evol , vol.21 , pp. 36-44
    • Tamura, K.1    Subramanian, S.2    Kumar, S.3
  • 88
    • 84875634162 scopus 로고    scopus 로고
    • Integrative genomics viewer (igv): High-performance genomics data visualization and exploration
    • Thorvaldsdóttir H, Robinson JT, Mesirov JP. 2013. Integrative genomics viewer (igv): high-performance genomics data visualization and exploration. Brief Bioinform. 14: 178-192.
    • (2013) Brief Bioinform , vol.14 , pp. 178-192
    • Thorvaldsdóttir, H.1    Robinson, J.T.2    Mesirov, J.P.3
  • 89
    • 1842408427 scopus 로고    scopus 로고
    • Transposition rate of the 412 retrotransposable element is independent of copy number in natural populations of Drosophila simulans
    • Vieira C, Biémont C. 1997. Transposition rate of the 412 retrotransposable element is independent of copy number in natural populations of Drosophila simulans. Mol Biol Evol. 14: 185-188.
    • (1997) Mol Biol Evol , vol.14 , pp. 185-188
    • Vieira, C.1    Biémont, C.2
  • 90
    • 1842522994 scopus 로고    scopus 로고
    • Transposable element dynamics in two sibling species: Drosophila melanogaster and Drosophila simulans
    • Vieira C, Biémont C. 2004. Transposable element dynamics in two sibling species: Drosophila melanogaster and Drosophila simulans. Genetica 120: 115-123.
    • (2004) Genetica , vol.120 , pp. 115-123
    • Vieira, C.1    Biémont, C.2
  • 91
    • 0032823323 scopus 로고    scopus 로고
    • Wake up of transposable elements following Drosophila simulans worldwide colonization
    • Vieira C, Lepetit D, Dumont S, Biémont C. 1999. Wake up of transposable elements following Drosophila simulans worldwide colonization. Mol Biol Evol. 16: 1251-1255.
    • (1999) Mol Biol Evol , vol.16 , pp. 1251-1255
    • Vieira, C.1    Lepetit, D.2    Dumont, S.3    Biémont, C.4
  • 92
    • 0035986886 scopus 로고    scopus 로고
    • Evolution of genome size in Drosophila. Is the invader's genome being invaded by transposable elements?
    • Vieira C, et al. 2002. Evolution of genome size in Drosophila.. Is the invader's genome being invaded by transposable elements? Mol Biol Evol. 19: 1154-1161.
    • (2002) Mol Biol Evol , vol.19 , pp. 1154-1161
    • Vieira, C.1
  • 93
    • 84866370634 scopus 로고    scopus 로고
    • Horizontal transposon transfer in eukarya: Detection, bias, and perspectives
    • Wallau GL, Ortiz MF, Loreto ELS. 2012. Horizontal transposon transfer in eukarya: detection, bias, and perspectives. Genome Biol Evol. 4: 689-699.
    • (2012) Genome Biol Evol , vol.4 , pp. 689-699
    • Wallau, G.L.1    Ortiz, M.F.2    Loreto, E.L.S.3
  • 94
    • 70350664664 scopus 로고    scopus 로고
    • Multiple testing in genomewide association studies via hiddenMarkovmodels
    • Wei Z, Sun W, Wang K, Hakonarson H. 2009. Multiple testing in genomewide association studies via hiddenMarkovmodels. Bioinformatics 25: 2802-2808.
    • (2009) Bioinformatics , vol.25 , pp. 2802-2808
    • Wei, Z.1    Sun, W.2    Wang, K.3    Hakonarson, H.4
  • 95
    • 70350227349 scopus 로고    scopus 로고
    • Conjugation genes are common throughout the genus Rickettsia and are transmitted horizontally
    • Weinert LA, Welch JJ, Jiggins FM. 2009. Conjugation genes are common throughout the genus Rickettsia and are transmitted horizontally. Proc R Soc B. 276: 3619-3627.
    • (2009) Proc R Soc B. , vol.276 , pp. 3619-3627
    • Weinert, L.A.1    Welch, J.J.2    Jiggins, F.M.3
  • 96
    • 43049101093 scopus 로고    scopus 로고
    • Calibrating the avian molecular clock
    • Weir JT, Schluter D. 2008. Calibrating the avian molecular clock. Mol Ecol. 17: 2321-2328.
    • (2008) Mol Ecol , vol.17 , pp. 2321-2328
    • Weir, J.T.1    Schluter, D.2
  • 97
    • 36249023071 scopus 로고    scopus 로고
    • A unified classification system for eukaryotic transposable elements
    • Wicker T, et al. 2007. A unified classification system for eukaryotic transposable elements. Nat Rev Genet. 8: 973-982.
    • (2007) Nat Rev Genet , vol.8 , pp. 973-982
    • Wicker, T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.