메뉴 건너뛰기




Volumn 190, Issue 2, 2012, Pages 813-825

Inferring the history of interchromosomal gene transposition in Drosophila using n-dimensional parsimony

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; DROSOPHILA; GENE; GENE ACTIVITY; GENE DOSAGE; GENE DUPLICATION; GENE FUNCTION; GENE LOCUS; GENE SEQUENCE; GENOME ANALYSIS; INTERCHROMOSOMAL GENE TRANSPOSITION; MOLECULAR EVOLUTION; NONHUMAN; PARSIMONY ANALYSIS; PHYLOGENY; PRIORITY JOURNAL; SEGREGATION ANALYSIS; SEQUENCE ANALYSIS; X CHROMOSOME;

EID: 84857433318     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.111.135947     Document Type: Article
Times cited : (17)

References (51)
  • 1
    • 0016813669 scopus 로고
    • The location of 5S (ribosomal) RNA genes in Drosophila hydei
    • Alonso, C., and H. D. Berendes, 1975 The location of 5S (ribosomal) RNA genes in Drosophila hydei. Chromosoma 51: 347-356.
    • (1975) Chromosoma , vol.51 , pp. 347-356
    • Alonso, C.1    Berendes, H.D.2
  • 2
    • 84857412444 scopus 로고    scopus 로고
    • Molecular population genetics and evolution of Drosophila meiosis genes
    • Anderson, J., W. Gilliland, and C. Langley, 2009 Molecular population genetics and evolution of Drosophila meiosis genes. Genetics 178: 477-487.
    • (2009) Genetics , vol.178 , pp. 477-487
    • Anderson, J.1    Gilliland, W.2    Langley, C.3
  • 3
    • 77957854239 scopus 로고    scopus 로고
    • Dosage compensation and demasculinization of X chromosomes in Drosophila
    • Bachtrog, D., N. R. T. Toda, and S. Lockton, 2010 Dosage compensation and demasculinization of X chromosomes in Drosophila. Curr. Biol. 20: 1476-1481.
    • (2010) Curr. Biol , vol.20 , pp. 1476-1481
    • Bachtrog, D.1    Toda, N.R.T.2    Lockton, S.3
  • 4
    • 34147128526 scopus 로고    scopus 로고
    • Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila
    • Bai, Y., C. Casola, C. Feschotte, and E. Betrán, 2007 Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila. Genome Biol. 8: R11.
    • (2007) Genome Biol , vol.8
    • Bai, Y.1    Casola, C.2    Feschotte, C.3    Betrán, E.4
  • 5
    • 0036906987 scopus 로고    scopus 로고
    • Retroposed new genes out of the X in Drosophila
    • Betrán, E., K. Thornton, and M. Long, 2002 Retroposed new genes out of the X in Drosophila. Genome Res. 12: 1854-1859.
    • (2002) Genome Res , vol.12 , pp. 1854-1859
    • Betrán, E.1    Thornton, K.2    Long, M.3
  • 6
    • 33749571076 scopus 로고    scopus 로고
    • Fast protein evolution and germ line expression of a Drosophila parental gene and its young retroposed paralog
    • Betrán, E., Y. Bai, and M. Motiwale, 2006 Fast protein evolution and germ line expression of a Drosophila parental gene and its young retroposed paralog. Mol. Biol. Evol. 23: 2191-2202.
    • (2006) Mol. Biol. Evol , vol.23 , pp. 2191-2202
    • Betrán, E.1    Bai, Y.2    Motiwale, M.3
  • 7
    • 37249085295 scopus 로고    scopus 로고
    • Genomescale analysis of positionally relocated genes
    • Bhutkar, A., S. Russo, T. Smith, and W. Gelbart, 2007 Genomescale analysis of positionally relocated genes. Genome Res. 17: 1880-1887.
    • (2007) Genome Res , vol.17 , pp. 1880-1887
    • Bhutkar, A.1    Russo, S.2    Smith, T.3    Gelbart, W.4
  • 8
    • 77956642088 scopus 로고    scopus 로고
    • Nonallelic gene conversion in the genus Drosophila
    • Casola, C., C. L. Ganote, and M. W. Hahn, 2010 Nonallelic gene conversion in the genus Drosophila. Genetics 185: 95-103.
    • (2010) Genetics , vol.185 , pp. 95-103
    • Casola, C.1    Ganote, C.L.2    Hahn, M.W.3
  • 9
    • 47149117454 scopus 로고    scopus 로고
    • Evolution of genes and genomes on the Drosophila phylogeny
    • Clark, A. G., M. B. Eisen, D. R. Smith, C. M. Bergman, B. Oliver et al., 2007 Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.
    • (2007) Nature , vol.450 , pp. 203-218
    • Clark, A.G.1    Eisen, M.B.2    Smith, D.R.3    Bergman, C.M.4    Oliver, B.5
  • 10
    • 79953223739 scopus 로고    scopus 로고
    • The resolution of sexual antagonism by gene duplication
    • Connallon, T., and A. G. Clark, 2011 The resolution of sexual antagonism by gene duplication. Genetics 187: 919-937.
    • (2011) Genetics , vol.187 , pp. 919-937
    • Connallon, T.1    Clark, A.G.2
  • 11
    • 33847611887 scopus 로고    scopus 로고
    • Not born equal: Increased rate asymmetry in relocated and retrotransposed rodent gene duplicates
    • Cusack, B., and K. H. Wolfe, 2007 Not born equal: increased rate asymmetry in relocated and retrotransposed rodent gene duplicates. Mol. Biol. Evol. 24: 679-686.
    • (2007) Mol. Biol. Evol , vol.24 , pp. 679-686
    • Cusack, B.1    Wolfe, K.H.2
  • 12
    • 34247387864 scopus 로고    scopus 로고
    • Retrogene movement within- and between-chromosomes in the evolution of Drosophila genomes
    • Dai, H., T. Yoshimatsu, and M. Long, 2006 Retrogene movement within- and between-chromosomes in the evolution of Drosophila genomes. Gene 385: 96-102.
    • (2006) Gene , vol.385 , pp. 96-102
    • Dai, H.1    Yoshimatsu, T.2    Long, M.3
  • 13
    • 33645981936 scopus 로고    scopus 로고
    • A hybrid micro-macroevolutionary approach to gene tree reconstruction
    • Durand, D., B. Halldorsson, and B. Vernot, 2006 A hybrid micro-macroevolutionary approach to gene tree reconstruction. J. Comput. Biol. 13: 320-335.
    • (2006) J. Comput. Biol , vol.13 , pp. 320-335
    • Durand, D.1    Halldorsson, B.2    Vernot, B.3
  • 14
    • 60849139395 scopus 로고    scopus 로고
    • GOrilla: A tool for discovery and visualization of enriched GO terms in ranked gene lists
    • Eden, E., R. Navon, I. Steinfeld, D. Lipson, and Z. Yakhini, 2009 GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 10: 48.
    • (2009) BMC Bioinformatics , vol.10 , pp. 48
    • Eden, E.1    Navon, R.2    Steinfeld, I.3    Lipson, D.4    Yakhini, Z.5
  • 15
    • 1642475221 scopus 로고    scopus 로고
    • Extensive gene traffic on the mammalian X chromosome
    • Emerson, J. J., H. Kaessmann, E. Betrán, and M. Long, 2004 Extensive gene traffic on the mammalian X chromosome. Science 303: 537-540.
    • (2004) Science , vol.303 , pp. 537-540
    • Emerson, J.J.1    Kaessmann, H.2    Betrán, E.3    Long, M.4
  • 16
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • Enright, A. J., S. Van Dongen, and C. A. Ouzounis, 2002 An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30: 1575-1584.
    • (2002) Nucleic Acids Res , vol.30 , pp. 1575-1584
    • Enright, A.J.1    van Dongen, S.2    Ouzounis, C.A.3
  • 17
    • 84959795073 scopus 로고
    • Phylogenetic analysis under Dollo's law
    • Farris, J. S., 1977 Phylogenetic analysis under Dollo's law. Syst. Zool. 26: 77-88.
    • (1977) Syst. Zool , vol.26 , pp. 77-88
    • Farris, J.S.1
  • 18
    • 84991160495 scopus 로고
    • Histone gene transposition in the phylogeny of the Drosophila obscura group
    • Felger, I., and W. Pinsker, 1987 Histone gene transposition in the phylogeny of the Drosophila obscura group. J. Zool. Syst. Evol. Res. 25: 127-140.
    • (1987) J. Zool. Syst. Evol. Res , vol.25 , pp. 127-140
    • Felger, I.1    Pinsker, W.2
  • 19
    • 0018864253 scopus 로고
    • The actin genes of Drosophila: A dispersed multigene family
    • Fyrberg, E., K. Kindle, N. Davidson, and A. Sodja, 1980 The actin genes of Drosophila: a dispersed multigene family. Cell 19: 365-378.
    • (1980) Cell , vol.19 , pp. 365-378
    • Fyrberg, E.1    Kindle, K.2    Davidson, N.3    Sodja, A.4
  • 20
    • 79954687738 scopus 로고    scopus 로고
    • Intralocus sexual conflict resolved through gene duplication
    • Gallach, M., and E. Betrán, 2011 Intralocus sexual conflict resolved through gene duplication. Trends Ecol. Evol. 26: 222-228.
    • (2011) Trends Ecol. Evol , vol.26 , pp. 222-228
    • Gallach, M.1    Betrán, E.2
  • 21
    • 36048950933 scopus 로고    scopus 로고
    • Gene family evolution across 12 Drosophila genomes
    • Hahn, M. W., M. V. Han, and S.-G. Han, 2007 Gene family evolution across 12 Drosophila genomes. PLoS Genet. 3: e197.
    • (2007) PLoS Genet , vol.3
    • Hahn, M.W.1    Han, M.V.2    Han, S.-G.3
  • 22
    • 61949351485 scopus 로고    scopus 로고
    • Identifying parent-daughter relationships among duplicated genes
    • Han, M. V., and M. W. Hahn, 2009 Identifying parent-daughter relationships among duplicated genes. Pac. Symp. Biocomput. 2009: 114-125.
    • (2009) Pac. Symp. Biocomput , vol.2009 , pp. 114-125
    • Han, M.V.1    Hahn, M.W.2
  • 23
    • 66049138497 scopus 로고    scopus 로고
    • Adaptive evolution of young gene duplicates in mammals
    • Han, M. V., J. Demuth, C. McGrath, C. Casola, and M. W. Hahn, 2009 Adaptive evolution of young gene duplicates in mammals. Genome Res. 19: 859-867.
    • (2009) Genome Res , vol.19 , pp. 859-867
    • Han, M.V.1    Demuth, J.2    McGrath, C.3    Casola, C.4    Hahn, M.W.5
  • 24
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang, D. W., B. T. Sherman, and R. A. Lempicki, 2008 Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4: 44-57.
    • (2008) Nat. Protoc , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 25
    • 35649007348 scopus 로고    scopus 로고
    • Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution
    • Jiang, Z., H. Tang, M. Ventura, M. F. Cardone, T. Marques-Bonet et al., 2007 Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution. Nat. Genet. 39: 1361-1368.
    • (2007) Nat. Genet , vol.39 , pp. 1361-1368
    • Jiang, Z.1    Tang, H.2    Ventura, M.3    Cardone, M.F.4    Marques-Bonet, T.5
  • 26
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: Improvement in accuracy of multiple sequence alignment
    • Katoh, K., K.-I. Kuma, H. Toh, and T. Miyata, 2005 MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33: 511-518.
    • (2005) Nucleic Acids Res , vol.33 , pp. 511-518
    • Katoh, K.1    Kuma, K.-I.2    Toh, H.3    Miyata, T.4
  • 27
    • 1642399822 scopus 로고    scopus 로고
    • Male-biased mutation, sex linkage, and the rate of adaptive evolution
    • Kirkpatrick, M., and D. W. Hall, 2004 Male-biased mutation, sex linkage, and the rate of adaptive evolution. Evolution 58: 437-440.
    • (2004) Evolution , vol.58 , pp. 437-440
    • Kirkpatrick, M.1    Hall, D.W.2
  • 28
    • 39749094829 scopus 로고    scopus 로고
    • On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees
    • Marques-Bonet, T., J. Sànchez-Ruiz, L. Armengol, R. Khaja, J. Bertranpetit et al., 2007 On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees. Genome Biol. 8: R230.
    • (2007) Genome Biol , vol.8
    • Marques-Bonet, T.1    Sànchez-Ruiz, J.2    Armengol, L.3    Khaja, R.4    Bertranpetit, J.5
  • 29
    • 33748490697 scopus 로고    scopus 로고
    • Gene transposition as a cause of hybrid sterility in Drosophila
    • Masly, J. P., C. Jones, M. Noor, J. Locke, and H. A. Orr, 2006 Gene transposition as a cause of hybrid sterility in Drosophila. Science 313: 1448-1450.
    • (2006) Science , vol.313 , pp. 1448-1450
    • Masly, J.P.1    Jones, C.2    Noor, M.3    Locke, J.4    Orr, H.A.5
  • 30
    • 77949433075 scopus 로고    scopus 로고
    • Genetic conflict and sex chromosome evolution
    • Meiklejohn, C., and Y. Tao, 2010 Genetic conflict and sex chromosome evolution. Trends Ecol. Evol. 25: 215-223.
    • (2010) Trends Ecol. Evol , vol.25 , pp. 215-223
    • Meiklejohn, C.1    Tao, Y.2
  • 31
    • 73649093539 scopus 로고    scopus 로고
    • A complex suite of forces drives gene traffic from Drosophila X chromosomes
    • Meisel, R. P., M. V. Han, and M. W. Hahn, 2009 A complex suite of forces drives gene traffic from Drosophila X chromosomes. Genome Biol. Evol. 1: 176-188.
    • (2009) Genome Biol. Evol , vol.1 , pp. 176-188
    • Meisel, R.P.1    Han, M.V.2    Hahn, M.W.3
  • 32
    • 77955003456 scopus 로고    scopus 로고
    • Adaptive evolution of genes duplicated from the Drosophila pseudoobscura neo-X chromosome
    • Meisel, R., B. Hilldorfer, J. Koch, S. Lockton, and S. Schaeffer, 2010 Adaptive evolution of genes duplicated from the Drosophila pseudoobscura neo-X chromosome. Mol. Biol. Evol. 27: 1963-1978.
    • (2010) Mol. Biol. Evol , vol.27 , pp. 1963-1978
    • Meisel, R.1    Hilldorfer, B.2    Koch, J.3    Lockton, S.4    Schaeffer, S.5
  • 33
    • 77953887346 scopus 로고    scopus 로고
    • The contribution of gene movement to the two rules of speciation
    • Moyle, L. C., C. D. Muir, M. V. Han, and M. W. Hahn, 2010 The contribution of gene movement to the "two rules of speciation". Evolution 64: 1541-1557.
    • (2010) Evolution , vol.64 , pp. 1541-1557
    • Moyle, L.C.1    Muir, C.D.2    Han, M.V.3    Hahn, M.W.4
  • 34
    • 0002084648 scopus 로고
    • Bearings of the 'Drosophila' work on systematics
    • edited by J. Huxley. Clarendon Press, Oxford
    • Muller, H. J., 1940 Bearings of the 'Drosophila' work on systematics, pp. 185-268 in The New Systematics, edited by J. Huxley. Clarendon Press, Oxford.
    • (1940) The New Systematics , pp. 185-268
    • Muller, H.J.1
  • 35
    • 0020790321 scopus 로고
    • Population genetics of multigene families that are dispersed into two or more chromosomes
    • Ohta, T., and G. Dover, 1983 Population genetics of multigene families that are dispersed into two or more chromosomes. Proc. Natl. Acad. Sci. USA 80: 4079-4083.
    • (1983) Proc. Natl. Acad. Sci. USA , vol.80 , pp. 4079-4083
    • Ohta, T.1    Dover, G.2
  • 36
    • 0030814489 scopus 로고    scopus 로고
    • Germ line transposition of the copia retrotransposon in Drosophila melanogaster is restricted to males by tissue-specific control of copia RNA levels
    • Pasyukova, E., S. Nuzhdin, W. Li, and A. J. Flavell, 1997 Germ line transposition of the copia retrotransposon in Drosophila melanogaster is restricted to males by tissue-specific control of copia RNA levels. Mol. Gen. Genet. 255: 115-124.
    • (1997) Mol. Gen. Genet , vol.255 , pp. 115-124
    • Pasyukova, E.1    Nuzhdin, S.2    Li, W.3    Flavell, A.J.4
  • 37
    • 43249118306 scopus 로고    scopus 로고
    • Chromosomal gene movements reflect the recent origin and biology of therian sex chromosomes
    • Potrzebowski, L., N. Vinckenbosch, A. C. Marques, F. Chalmel, B. Jégou et al., 2008 Chromosomal gene movements reflect the recent origin and biology of therian sex chromosomes. PLoS Biol. 6: e80.
    • (2008) PLoS Biol , vol.6
    • Potrzebowski, L.1    Vinckenbosch, N.2    Marques, A.C.3    Chalmel, F.4    Jégou, B.5
  • 38
    • 0037626724 scopus 로고    scopus 로고
    • Low occurrence of gene transposition events during the evolution of the genus Drosophila
    • Ranz, J., J. Gonzalez, F. Casals, and A. Ruiz, 2003 Low occurrence of gene transposition events during the evolution of the genus Drosophila. Evolution 57: 1325-1335.
    • (2003) Evolution , vol.57 , pp. 1325-1335
    • Ranz, J.1    Gonzalez, J.2    Casals, F.3    Ruiz, A.4
  • 39
    • 0021554565 scopus 로고
    • Sex chromosomes and the evolution of sexual dimorphism
    • Rice, W., 1984 Sex chromosomes and the evolution of sexual dimorphism. Evolution 38: 735-742.
    • (1984) Evolution , vol.38 , pp. 735-742
    • Rice, W.1
  • 40
    • 0019122227 scopus 로고
    • A dispersed multigene family encoding tubulin in Drosophila melanogaster
    • Sánchez, F., J. Natzle, D. Cleveland, M. Kirschner, and B. McCarthy, 1980 A dispersed multigene family encoding tubulin in Drosophila melanogaster. Cell 22: 845-854.
    • (1980) Cell , vol.22 , pp. 845-854
    • Sánchez, F.1    Natzle, J.2    Cleveland, D.3    Kirschner, M.4    McCarthy, B.5
  • 41
    • 0000459582 scopus 로고
    • Locating the vertices of a Steiner tree in an arbitrary metric space
    • Sankoff, D., and P. Rousseau, 1975 Locating the vertices of a Steiner tree in an arbitrary metric space. Math. Program. 9: 240-246.
    • (1975) Math. Program , vol.9 , pp. 240-246
    • Sankoff, D.1    Rousseau, P.2
  • 42
    • 52049125422 scopus 로고    scopus 로고
    • Polytene chromosomal maps of 11 Drosophila species: The order of genomic scaffolds inferred from genetic and physical maps
    • Schaeffer, S., A. Bhutkar, B. McAllister, M. Matsuda, L. Matzkin et al., 2008 Polytene chromosomal maps of 11 Drosophila species: the order of genomic scaffolds inferred from genetic and physical maps. Genetics 179: 1601-1655.
    • (2008) Genetics , vol.179 , pp. 1601-1655
    • Schaeffer, S.1    Bhutkar, A.2    McAllister, B.3    Matsuda, M.4    Matzkin, L.5
  • 43
    • 83055168359 scopus 로고    scopus 로고
    • Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster
    • Schrider, D. R., K. A. Stevens, C. M. Cardeno, C. H. Langley, and M. W. Hahn, 2011 Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster. Genome Res. 21: 2087-2095.
    • (2011) Genome Res , vol.21 , pp. 2087-2095
    • Schrider, D.R.1    Stevens, K.A.2    Cardeno, C.M.3    Langley, C.H.4    Hahn, M.W.5
  • 44
    • 36049039511 scopus 로고    scopus 로고
    • Demasculinization of X chromosomes in the Drosophila genus
    • Sturgill, D., Y. Zhang, M. Parisi, and B. Oliver, 2007 Demasculinization of X chromosomes in the Drosophila genus. Nature 450: 238-241.
    • (2007) Nature , vol.450 , pp. 238-241
    • Sturgill, D.1    Zhang, Y.2    Parisi, M.3    Oliver, B.4
  • 45
    • 77955903376 scopus 로고    scopus 로고
    • Convergently recruited nuclear transport retrogenes are male biased in expression and evolving under positive selection in Drosophila
    • Tracy, C., J. Rio, M. Motiwale, S. Christensen, and E. Betrán, 2010 Convergently recruited nuclear transport retrogenes are male biased in expression and evolving under positive selection in Drosophila. Genetics 184: 1067-1076.
    • (2010) Genetics , vol.184 , pp. 1067-1076
    • Tracy, C.1    Rio, J.2    Motiwale, M.3    Christensen, S.4    Betrán, E.5
  • 46
    • 66049085185 scopus 로고    scopus 로고
    • General gene movement off the X chromosome in the Drosophila genus
    • Vibranovski, M. D., Y. Zhang, and M. Long, 2009 General gene movement off the X chromosome in the Drosophila genus. Genome Res. 19: 897-903.
    • (2009) Genome Res , vol.19 , pp. 897-903
    • Vibranovski, M.D.1    Zhang, Y.2    Long, M.3
  • 47
  • 48
    • 0037407075 scopus 로고    scopus 로고
    • Sexual antagonism and X inactivation-the SAXI hypothesis
    • Wu, C.-I., and Y. E. Xu, 2003 Sexual antagonism and X inactivation-the SAXI hypothesis. Trends Genet. 19: 243-247.
    • (2003) Trends Genet , vol.19 , pp. 243-247
    • Wu, C.-I.1    Xu, Y.E.2
  • 49
    • 0031897964 scopus 로고    scopus 로고
    • Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
    • Yang, Z., 1998 Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15: 568-573.
    • (1998) Mol. Biol. Evol , vol.15 , pp. 568-573
    • Yang, Z.1
  • 50
    • 78649283800 scopus 로고    scopus 로고
    • Agedependent chromosomal distribution of male-biased genes in Drosophila
    • Zhang, Y., M. Vibranovski, B. Krinsky, and M. Long, 2010 Agedependent chromosomal distribution of male-biased genes in Drosophila. Genome Res. 20: 1526-1533.
    • (2010) Genome Res , vol.20 , pp. 1526-1533
    • Zhang, Y.1    Vibranovski, M.2    Krinsky, B.3    Long, M.4
  • 51
    • 2442418972 scopus 로고    scopus 로고
    • Genomic background predicts the fate of duplicated genes: Evidence from the yeast genome
    • Zhang, Z., and H. Kishino, 2004 Genomic background predicts the fate of duplicated genes: evidence from the yeast genome. Genetics 166: 1995-1999.
    • (2004) Genetics , vol.166 , pp. 1995-1999
    • Zhang, Z.1    Kishino, H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.