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Volumn 3, Issue 10, 2007, Pages 2007-2013

Adaptive gene expression divergence inferred from population genomics

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; DNA FLANKING REGION; DROSOPHILA; DROSOPHILA MELANOGASTER; DROSOPHILA SIMULANS; DROSOPHILA YAKUBA; EVOLUTIONARY ADAPTATION; FEMALE; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; MALE; MOLECULAR GENETICS; MOLECULAR PHYLOGENY; NONHUMAN; POPULATION GENETICS;

EID: 35948998931     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0030187     Document Type: Article
Times cited : (44)

References (38)
  • 1
    • 0024389204 scopus 로고
    • Molecular basis of evolutionary adaptation at the lactate dehydrogenase-B locus in the fish Fundulus heteroclitus
    • Crawford DL, Powers DA (1989) Molecular basis of evolutionary adaptation at the lactate dehydrogenase-B locus in the fish Fundulus heteroclitus. Proc Natl Acad Sci U S A 86: 9365-9369.
    • (1989) Proc Natl Acad Sci U S A , vol.86 , pp. 9365-9369
    • Crawford, D.L.1    Powers, D.A.2
  • 2
    • 0036812208 scopus 로고    scopus 로고
    • Nucleotide polymorphism in the Est6 promoter, which is widespread in derived populations of Drosophila melanogaster, changes the level of Esterase 6 expressed in the male ejaculatory duct
    • Odgers WA, Aquadro CF, Coppin CW, Healy MJ, Oakeshott JG (2002) Nucleotide polymorphism in the Est6 promoter, which is widespread in derived populations of Drosophila melanogaster, changes the level of Esterase 6 expressed in the male ejaculatory duct. Genetics 162: 785-797.
    • (2002) Genetics , vol.162 , pp. 785-797
    • Odgers, W.A.1    Aquadro, C.F.2    Coppin, C.W.3    Healy, M.J.4    Oakeshott, J.G.5
  • 3
    • 19344372220 scopus 로고    scopus 로고
    • A neutral model of transcriptome evolution
    • doi:10.1371/journal.pbio.0020132
    • Khaitovich P, Weiss G, Lachmann M, Hellmann I, Enard W, et al. (2004) A neutral model of transcriptome evolution. PLoS Biol 2: e132. doi:10.1371/journal.pbio.0020132
    • (2004) PLoS Biol , vol.2
    • Khaitovich, P.1    Weiss, G.2    Lachmann, M.3    Hellmann, I.4    Enard, W.5
  • 4
    • 33644855479 scopus 로고    scopus 로고
    • Expression profiling in primates reveals a rapid evolution of human transcription factors
    • Gilad Y, Oshlack A, Smyth GK, Speed TP, White KP (2006) Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature 440: 242-245.
    • (2006) Nature , vol.440 , pp. 242-245
    • Gilad, Y.1    Oshlack, A.2    Smyth, G.K.3    Speed, T.P.4    White, K.P.5
  • 5
    • 0037313182 scopus 로고    scopus 로고
    • Evolution of gene expression in the Drosophila melanogaster subgroup
    • Rifkin SA, Kim J, White KP (2003) Evolution of gene expression in the Drosophila melanogaster subgroup. Nat Genet 33: 138-144.
    • (2003) Nat Genet , vol.33 , pp. 138-144
    • Rifkin, S.A.1    Kim, J.2    White, K.P.3
  • 6
    • 3042591076 scopus 로고    scopus 로고
    • Common pattern of evolution of gene expression level and protein sequence in Drosophila
    • Nuzhdin SV, Wayne ML, Harmon KL, McIntyre LM (2004) Common pattern of evolution of gene expression level and protein sequence in Drosophila. Mol Biol Evol 21: 1308-1317.
    • (2004) Mol Biol Evol , vol.21 , pp. 1308-1317
    • Nuzhdin, S.V.1    Wayne, M.L.2    Harmon, K.L.3    McIntyre, L.M.4
  • 8
    • 33646882592 scopus 로고    scopus 로고
    • Adaptive protein evolution and regulatory divergence in Drosophila
    • Good JM, Hayden CA, Wheeler TJ (2006) Adaptive protein evolution and regulatory divergence in Drosophila. Mol Biol Evol 23: 1101-1103.
    • (2006) Mol Biol Evol , vol.23 , pp. 1101-1103
    • Good, J.M.1    Hayden, C.A.2    Wheeler, T.J.3
  • 10
    • 35948995392 scopus 로고    scopus 로고
    • Coordinated evolution of coexpression gene clusters in the Drosophila transcriptome
    • In press
    • Mezey JG, Nuzhdin SV, Ye F, Jones CD (2007) Coordinated evolution of coexpression gene clusters in the Drosophila transcriptome. BMC Bioinformatics. In press.
    • (2007) BMC Bioinformatics
    • Mezey, J.G.1    Nuzhdin, S.V.2    Ye, F.3    Jones, C.D.4
  • 11
    • 35948940895 scopus 로고    scopus 로고
    • Population genomics: Whole-genome analysis of polymorphism and divergence in Drosophila simulans
    • doi:10.1371/journal.pbio. 0050310
    • Begun DJ, Holloway AK, Stevens KS, Hiller LW, Poh Y, Stevens KS, et al. (2007) Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol. 5: e310. doi:10.1371/journal.pbio. 0050310
    • (2007) PLoS Biol , vol.5
    • Begun, D.J.1    Holloway, A.K.2    Stevens, K.S.3    Hiller, L.W.4    Poh, Y.5    Stevens, K.S.6
  • 13
    • 0016220238 scopus 로고
    • The hitch-hiking effect of a favourable gene
    • Maynard Smith J, Haigh J (1974) The hitch-hiking effect of a favourable gene. Genet Res 23: 23-35.
    • (1974) Genet Res , vol.23 , pp. 23-35
    • Maynard Smith, J.1    Haigh, J.2
  • 14
    • 0026428610 scopus 로고
    • Adaptive protein evolution at the Adh locus in Drosophila
    • McDonald JH, Kreitman M (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
    • (1991) Nature , vol.351 , pp. 652-654
    • McDonald, J.H.1    Kreitman, M.2
  • 15
    • 19844365733 scopus 로고    scopus 로고
    • Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles
    • Gilad Y, Rifkin SA, Bertone P, Gerstein M, White KP (2005) Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res 15: 674-680.
    • (2005) Genome Res , vol.15 , pp. 674-680
    • Gilad, Y.1    Rifkin, S.A.2    Bertone, P.3    Gerstein, M.4    White, K.P.5
  • 17
    • 0029988881 scopus 로고    scopus 로고
    • Control of messenger RNA stability in higher eukaryotes
    • Ross J (1996) Control of messenger RNA stability in higher eukaryotes. Trends Genet 12: 171-175.
    • (1996) Trends Genet , vol.12 , pp. 171-175
    • Ross, J.1
  • 18
    • 0038343499 scopus 로고    scopus 로고
    • MicroRNA pathways in flies and worms: Growth, death, fat, stress, and timing
    • Ambros V (2003) MicroRNA pathways in flies and worms: growth, death, fat, stress, and timing. Cell 113: 673-676.
    • (2003) Cell , vol.113 , pp. 673-676
    • Ambros, V.1
  • 21
    • 0034978556 scopus 로고    scopus 로고
    • Highly expressed genes in yeast evolve slowly
    • Pal C, Papp B, Hurst LD (2001) Highly expressed genes in yeast evolve slowly. Genetics 158: 927-931.
    • (2001) Genetics , vol.158 , pp. 927-931
    • Pal, C.1    Papp, B.2    Hurst, L.D.3
  • 22
    • 0041817645 scopus 로고    scopus 로고
    • Translational selection and yeast proteome evolution
    • Akashi H (2003) Translational selection and yeast proteome evolution. Genetics 164: 1291-1303.
    • (2003) Genetics , vol.164 , pp. 1291-1303
    • Akashi, H.1
  • 24
    • 0037472685 scopus 로고    scopus 로고
    • Serine proteases and their homologs in the Drosophila melanogaster genome: An initial analysis of sequence conservation and phylogenetic relationships
    • Ross J, Jiang H, Kanost MR, Wang Y (2003) Serine proteases and their homologs in the Drosophila melanogaster genome: an initial analysis of sequence conservation and phylogenetic relationships. Gene 304: 117-131.
    • (2003) Gene , vol.304 , pp. 117-131
    • Ross, J.1    Jiang, H.2    Kanost, M.R.3    Wang, Y.4
  • 25
    • 27144491328 scopus 로고    scopus 로고
    • Adaptive evolution of non-coding DNA in Drosophila
    • Andolfatto P (2005) Adaptive evolution of non-coding DNA in Drosophila. Nature 437: 1149-1152.
    • (2005) Nature , vol.437 , pp. 1149-1152
    • Andolfatto, P.1
  • 26
    • 1542347028 scopus 로고    scopus 로고
    • Inference of positive and negative selection on the 59 regulatory regions of Drosophila genes
    • Kohn MH, Fang S, Wu CI (2004) Inference of positive and negative selection on the 59 regulatory regions of Drosophila genes. Mol Biol Evol 21: 374-383.
    • (2004) Mol Biol Evol , vol.21 , pp. 374-383
    • Kohn, M.H.1    Fang, S.2    Wu, C.I.3
  • 27
    • 33745583768 scopus 로고    scopus 로고
    • A genetic signature of interspecies variations in gene expression
    • Tirosh I, Weinberger A, Carmi M, Barkai N (2006) A genetic signature of interspecies variations in gene expression. Nat Genet 38: 830-834.
    • (2006) Nat Genet , vol.38 , pp. 830-834
    • Tirosh, I.1    Weinberger, A.2    Carmi, M.3    Barkai, N.4
  • 28
    • 0037504137 scopus 로고    scopus 로고
    • Sex-dependent gene expression and evolution of the Drosophila transcriptome
    • Ranz JM, Castillo-Davis CI, Meiklejohn CD, Hartl DL (2003) Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science 300: 1742-1745.
    • (2003) Science , vol.300 , pp. 1742-1745
    • Ranz, J.M.1    Castillo-Davis, C.I.2    Meiklejohn, C.D.3    Hartl, D.L.4
  • 29
    • 1342288026 scopus 로고    scopus 로고
    • affy-analysis of Affymetrix GeneChip data at the probe level
    • Gautier L, Cope L, Bolstad BM, Irizarry RA (2004) affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20: 307-315.
    • (2004) Bioinformatics , vol.20 , pp. 307-315
    • Gautier, L.1    Cope, L.2    Bolstad, B.M.3    Irizarry, R.A.4
  • 30
    • 28744458859 scopus 로고    scopus 로고
    • Bioconductor: Open software development for computational biology and bioinformatics
    • Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
    • (2004) Genome Biol , vol.5
    • Gentleman, R.C.1    Carey, V.J.2    Bates, D.M.3    Bolstad, B.4    Dettling, M.5
  • 31
    • 0031417707 scopus 로고    scopus 로고
    • Likelihood of ancestor states in adaptive radiation
    • Schluter D, Price T, Mooers AO, Ludwig D (1997) Likelihood of ancestor states in adaptive radiation. Evolution 51: 1699-1711.
    • (1997) Evolution , vol.51 , pp. 1699-1711
    • Schluter, D.1    Price, T.2    Mooers, A.O.3    Ludwig, D.4
  • 32
    • 35949000143 scopus 로고    scopus 로고
    • Efron B, Tibshirani RJ (1993) An introduction to the bootstrap.Cox DR, Hinkley DV, Reid N, Rubin DB, Silverman BWeditors. Boca Raton (Florida): Chapman & Hall/CRC.
    • Efron B, Tibshirani RJ (1993) An introduction to the bootstrap.Cox DR, Hinkley DV, Reid N, Rubin DB, Silverman BWeditors. Boca Raton (Florida): Chapman & Hall/CRC.
  • 33
    • 0022507362 scopus 로고
    • Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
    • Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3: 418-426.
    • (1986) Mol Biol Evol , vol.3 , pp. 418-426
    • Nei, M.1    Gojobori, T.2
  • 34
    • 0028267146 scopus 로고
    • Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation
    • Yang Z, Goldman N, Friday A (1994) Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol Biol Evol 11: 316-324.
    • (1994) Mol Biol Evol , vol.11 , pp. 316-324
    • Yang, Z.1    Goldman, N.2    Friday, A.3
  • 36
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22: 160-174.
    • (1985) J Mol Evol , vol.22 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 37
    • 0030000951 scopus 로고    scopus 로고
    • Excess amino acid polymorphism in mitochondrial DNA: Contrasts among genes from Drosophila, mice, and humans
    • Rand DM, Kann LM (1996) Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans. Mol Biol Evol 13: 735-748.
    • (1996) Mol Biol Evol , vol.13 , pp. 735-748
    • Rand, D.M.1    Kann, L.M.2
  • 38
    • 0028220048 scopus 로고
    • Synonymous codon usage in Drosophila melanogaster: Natural selection and translational accuracy
    • Akashi H (1994) Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics 136: 927-935.
    • (1994) Genetics , vol.136 , pp. 927-935
    • Akashi, H.1


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