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Volumn 21, Issue 1, 2004, Pages 36-44

Temporal Patterns of Fruit Fly (Drosophila) Evolution Revealed by Mutation Clocks

Author keywords

Drosophila; Evolutionary distance estimation; Molecular clock; Molecular evolution; Mutation rate; Speciation

Indexed keywords

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; DROSOPHILA; DROSOPHILA MELANOGASTER; DROSOPHILA SIMULANS; EVOLUTION; FOSSIL; GENE MUTATION; GENE SEQUENCE; MOLECULAR CLOCK; NONHUMAN; PALEOCLIMATE; POPULATION GENETICS;

EID: 1242352089     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msg236     Document Type: Article
Times cited : (490)

References (52)
  • 1
    • 0032978833 scopus 로고    scopus 로고
    • Positive selection drives the evolution of the Acp29AB accessory gland protein in Drosophila
    • Aguade, M. 1999. Positive selection drives the evolution of the Acp29AB accessory gland protein in Drosophila. Genetics 152:543-551.
    • (1999) Genetics , vol.152 , pp. 543-551
    • Aguade, M.1
  • 2
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5
  • 3
    • 0034751728 scopus 로고    scopus 로고
    • Rapid evolution of a cyclin A inhibitor gene, roughex, in Drosophila
    • Avedisov, S. N., I. B. Rogozin, E. V. Koonin, and B. J. Thomas. 2001. Rapid evolution of a cyclin A inhibitor gene, roughex, in Drosophila. Mol. Biol. Evol. 18:2110-2118.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 2110-2118
    • Avedisov, S.N.1    Rogozin, I.B.2    Koonin, E.V.3    Thomas, B.J.4
  • 4
    • 0034883255 scopus 로고    scopus 로고
    • Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences
    • Bergman, C. M., and M. Kreitman. 2001. Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences. Genome Res. 11:1335-1345.
    • (2001) Genome Res. , vol.11 , pp. 1335-1345
    • Bergman, C.M.1    Kreitman, M.2
  • 5
    • 0012301705 scopus 로고    scopus 로고
    • Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome
    • RESEARCH0086-0086
    • Bergman, C. M., B. D. Pfeiffer, D. E. Rincon-Limas, R. A. Hoskins, A. Gnirke et al. 2002. Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome. Genome Biol 3:RESEARCH0086-0086.
    • (2002) Genome Biol. , vol.3
    • Bergman, C.M.1    Pfeiffer, B.D.2    Rincon-Limas, D.E.3    Hoskins, R.A.4    Gnirke, A.5
  • 6
    • 0021723167 scopus 로고
    • Molecular evolution in Drosophila and the higher Diptera II. A time scale for fly evolution
    • Beverley, S. M., and A. C. Wilson. 1984. Molecular evolution in Drosophila and the higher Diptera II. A time scale for fly evolution. J. Mol. Evol. 21:1-13.
    • (1984) J. Mol. Evol. , vol.21 , pp. 1-13
    • Beverley, S.M.1    Wilson, A.C.2
  • 7
    • 0010558795 scopus 로고
    • Inversions in Hawaiian Drosophila
    • C. B. Krimbas and J. R. Powell, eds. CRC Press, Boca Raton, Fla
    • Carson, H. L. 1992. Inversions in Hawaiian Drosophila, Pp. 407-439 in C. B. Krimbas and J. R. Powell, eds. Drosophila inversion polymorphism. CRC Press, Boca Raton, Fla.
    • (1992) Drosophila Inversion Polymorphism , pp. 407-439
    • Carson, H.L.1
  • 8
    • 0002202674 scopus 로고
    • Geology and biogeography of Hawaii
    • W. L. Wagner and V. A. Funk, eds. Smithsonian Institution Press, Washington, D.C.
    • Carson, H. L., and D. A. Clauge. 1995. Geology and biogeography of Hawaii, Pp. 14-29 in W. L. Wagner and V. A. Funk, eds. Hawaiian biogeography: evolution on a hot spot archipelago. Smithsonian Institution Press, Washington, D.C.
    • (1995) Hawaiian Biogeography: Evolution on a Hot Spot Archipelago , pp. 14-29
    • Carson, H.L.1    Clauge, D.A.2
  • 9
    • 0035155844 scopus 로고    scopus 로고
    • Substitution rates in Drosophila nuclear genes: Implications for translational selection
    • Dunn, K. A., J. P. Bielawski, and Z. Yang. 2001. Substitution rates in Drosophila nuclear genes: implications for translational selection. Genetics 157:295-305.
    • (2001) Genetics , vol.157 , pp. 295-305
    • Dunn, K.A.1    Bielawski, J.P.2    Yang, Z.3
  • 10
    • 0029910046 scopus 로고    scopus 로고
    • Historical selection, amino acid polymorphism and lineage-specific divergence at the G6pd locus in Drosophila melanogaster and D. simulans
    • Eanes, W. F., M. Kirchner, J. Yoon, C. H. Biermann, I. N. Wang et al. 1996. Historical selection, amino acid polymorphism and lineage-specific divergence at the G6pd locus in Drosophila melanogaster and D. simulans. Genetics 144:1027-1041.
    • (1996) Genetics , vol.144 , pp. 1027-1041
    • Eanes, W.F.1    Kirchner, M.2    Yoon, J.3    Biermann, C.H.4    Wang, I.N.5
  • 11
    • 0022022042 scopus 로고
    • Estimating divergence times of Drosophila species from DNA-sequence comparisons
    • Easteal, S., and J. G. Oakeshott. 1985. Estimating divergence times of Drosophila species from DNA-sequence comparisons. Mol. Biol. Evol. 2:87-91.
    • (1985) Mol. Biol. Evol. , vol.2 , pp. 87-91
    • Easteal, S.1    Oakeshott, J.G.2
  • 12
    • 0035729730 scopus 로고    scopus 로고
    • Phylogenetic utility of mitochondrial COI and nuclear Gpdh genes in Drosophila
    • Goto, S. G., and M. T. Kimura. 2001. Phylogenetic utility of mitochondrial COI and nuclear Gpdh genes in Drosophila. Mol. Phylogenet. Evol. 18:404-422.
    • (2001) Mol. Phylogenet. Evol. , vol.18 , pp. 404-422
    • Goto, S.G.1    Kimura, M.T.2
  • 13
    • 0002083093 scopus 로고
    • Amber fossil Drosophilidae (Diptera), with particular reference to the Hispaniolan taxa
    • Grimaldi, D. A. 1987. Amber fossil Drosophilidae (Diptera), with particular reference to the Hispaniolan taxa. Am. Mus. Novitates 2880:1-23.
    • (1987) Am. Mus. Novitates , vol.2880 , pp. 1-23
    • Grimaldi, D.A.1
  • 14
    • 0037383240 scopus 로고    scopus 로고
    • Genomic clocks and evolutionary timescales
    • Hedges, S. B., and S. Kumar. 2003. Genomic clocks and evolutionary timescales. Trends Genet. 19:200-206.
    • (2003) Trends Genet. , vol.19 , pp. 200-206
    • Hedges, S.B.1    Kumar, S.2
  • 15
    • 0030845926 scopus 로고    scopus 로고
    • Comparative evolutionary rates of introns and exons in murine rodents
    • Hughes, A. L., and M. Yeager. 1997. Comparative evolutionary rates of introns and exons in murine rodents. J. Mol. Evol. 45:125-130.
    • (1997) J. Mol. Evol. , vol.45 , pp. 125-130
    • Hughes, A.L.1    Yeager, M.2
  • 16
    • 0012341115 scopus 로고    scopus 로고
    • The transposable elements of the Drosophila melanogaster euchromatin: A genomics perspective
    • RESEARCH0084-0084
    • Kaminker, J. S., C. M. Bergman, B. Kronmiller, J. Carlson, R. Svirskas et al. 2002. The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol. 3:RESEARCH0084-0084.
    • (2002) Genome Biol. , vol.3
    • Kaminker, J.S.1    Bergman, C.M.2    Kronmiller, B.3    Carlson, J.4    Svirskas, R.5
  • 17
    • 0002136593 scopus 로고
    • A Review of polar climatic evolution during the Neogene, based on the marine sediment record
    • E. S. Vrba, G. H. Denton, T. C. Partridge and L. H. Burckle, eds. Yale University Press, New Heaven, Conn
    • Kennett, J. P. 1995. A Review of polar climatic evolution during the Neogene, based on the marine sediment record, Pp. 49-64 in E. S. Vrba, G. H. Denton, T. C. Partridge and L. H. Burckle, eds. Paleoclimate and evolution, with emphasis on human origins. Yale University Press, New Heaven, Conn.
    • (1995) Paleoclimate and Evolution, with Emphasis on Human Origins , pp. 49-64
    • Kennett, J.P.1
  • 19
    • 0034923337 scopus 로고    scopus 로고
    • Disparity index: A simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences
    • Kumar, S., and S. R. Gadagkar. 2001. Disparity index: a simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences. Genetics 158:1321-1327.
    • (2001) Genetics , vol.158 , pp. 1321-1327
    • Kumar, S.1    Gadagkar, S.R.2
  • 21
    • 0000792280 scopus 로고
    • Historical biogeography of the Drosophila-Melanogaster species subgroup
    • Lachaise, D., M. L. Cariou, J. R. David, F. Lemeunier, L. Tsacas et al. 1988. Historical biogeography of the Drosophila-Melanogaster species subgroup. Evol. Biol. 22:159-225.
    • (1988) Evol. Biol. , vol.22 , pp. 159-225
    • Lachaise, D.1    Cariou, M.L.2    David, J.R.3    Lemeunier, F.4    Tsacas, L.5
  • 22
    • 0036153896 scopus 로고    scopus 로고
    • Cytoplasmic localization and evolutionary conservation of MEI-218, a protein required for meiotic crossing-over in Drosophila
    • Manheim, E. A., J. K. Jang, D. Dominic, and K. S. McKim. 2002. Cytoplasmic localization and evolutionary conservation of MEI-218, a protein required for meiotic crossing-over in Drosophila. Mol. Biol. Cell 13:84-95.
    • (2002) Mol. Biol. Cell , vol.13 , pp. 84-95
    • Manheim, E.A.1    Jang, J.K.2    Dominic, D.3    McKim, K.S.4
  • 23
    • 0027153966 scopus 로고
    • Codon usage bias and base composition of nuclear genes in Drosophila
    • Moriyama, E. N., and D. L. Hartl. 1993. Codon usage bias and base composition of nuclear genes in Drosophila. Genetics 134:847-858.
    • (1993) Genetics , vol.134 , pp. 847-858
    • Moriyama, E.N.1    Hartl, D.L.2
  • 25
    • 0036355477 scopus 로고    scopus 로고
    • Phylogeny of the subgenus sophophora (Diptera: Drosophilidae) based on combined analysis of nuclear and mitochondrial sequences
    • O'Grady, P. M., and M. G. Kidwell. 2002. Phylogeny of the subgenus sophophora (Diptera: Drosophilidae) based on combined analysis of nuclear and mitochondrial sequences. Mol. Phylogenet. Evol. 22:442-453.
    • (2002) Mol. Phylogenet. Evol. , vol.22 , pp. 442-453
    • O'Grady, P.M.1    Kidwell, M.G.2
  • 26
    • 0031891484 scopus 로고    scopus 로고
    • High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups
    • Petrov, D. A., and D. L. Hartl. 1998. High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups. Mol. Biol. Evol. 15:293-302.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 293-302
    • Petrov, D.A.1    Hartl, D.L.2
  • 28
    • 0037560021 scopus 로고    scopus 로고
    • Switch in codon bias and increased rates of amino acid substitution in the Drosophila saltans species group
    • Rodriguez-Trelles, F., R. Tarrio, and F. J. Ayala. 1999. Switch in codon bias and increased rates of amino acid substitution in the Drosophila saltans species group. Genetics 153:339-350.
    • (1999) Genetics , vol.153 , pp. 339-350
    • Rodriguez-Trelles, F.1    Tarrio, R.2    Ayala, F.J.3
  • 29
    • 0033938993 scopus 로고    scopus 로고
    • Fluctuating mutation bias and the evolution of base composition in Drosophila
    • -. 2000. Fluctuating mutation bias and the evolution of base composition in Drosophila. J. Mol. Evol. 50:1-10.
    • (2000) J. Mol. Evol. , vol.50 , pp. 1-10
  • 30
    • 0035949471 scopus 로고    scopus 로고
    • Erratic overdispersion of three molecular clocks: GPDH, SOD, and XDH
    • -. 2001a. Erratic overdispersion of three molecular clocks: GPDH, SOD, and XDH. Proc. Natl. Acad. Sci. USA 98:11405-11410.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 11405-11410
  • 31
    • 0034826141 scopus 로고    scopus 로고
    • Xanthine dehydrogenase (XDH): Episodic evolution of a "neutral" protein
    • -. 2001b. Xanthine dehydrogenase (XDH): episodic evolution of a "neutral" protein. J. Mol. Evol. 53:485-495.
    • (2001) J. Mol. Evol. , vol.53 , pp. 485-495
  • 32
    • 0025966049 scopus 로고
    • Rates of DNA change and phylogeny from the DNA sequences of the alcohol dehydrogenase gene for five closely related species of Hawaiian Drosophila
    • Rowan, R. G., and J. A. Hunt. 1991. Rates of DNA change and phylogeny from the DNA sequences of the alcohol dehydrogenase gene for five closely related species of Hawaiian Drosophila. Mol. Biol. Evol. 8:49-70.
    • (1991) Mol. Biol. Evol. , vol.8 , pp. 49-70
    • Rowan, R.G.1    Hunt, J.A.2
  • 33
    • 0028910659 scopus 로고
    • Molecular phylogeny and divergence times of drosophilid species
    • Russo, C. A. M., N. Takezaki, and M. Nei. 1995. Molecular phylogeny and divergence times of drosophilid species. Mol. Biol. Evol. 12:391-404.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 391-404
    • Russo, C.A.M.1    Takezaki, N.2    Nei, M.3
  • 34
    • 0023650543 scopus 로고
    • The Codon Adaptation Index - A measure of directional synonymous codon usage bias, and its potential applications
    • Sharp, P. M., and W. H. Li. 1987. The Codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15:1281-1295.
    • (1987) Nucleic Acids Res. , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 35
    • 0024591558 scopus 로고
    • On the rate of DNA sequence evolution in Drosophila
    • -. 1989. On the rate of DNA sequence evolution in Drosophila. J. Mol. Evol. 28:398-402.
    • (1989) J. Mol. Evol. , vol.28 , pp. 398-402
  • 36
    • 0024116811 scopus 로고
    • Silent sites in Drosophila genes are not neutral - Evidence of selection among synonymous codons
    • Shields, D. C., P. M. Sharp, D. G. Higgins, and F. Wright. 1988. Silent sites in Drosophila genes are not neutral-evidence of selection among synonymous codons. Mol. Biol. Evol. 5:704-716.
    • (1988) Mol. Biol. Evol. , vol.5 , pp. 704-716
    • Shields, D.C.1    Sharp, P.M.2    Higgins, D.G.3    Wright, F.4
  • 37
    • 0033804947 scopus 로고    scopus 로고
    • Horizontal transfer and selection in the evolution of P elements
    • Silva, J. C., and M. G. Kidwell. 2000. Horizontal transfer and selection in the evolution of P elements. Mol. Biol. Evol. 17:1542-1557.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1542-1557
    • Silva, J.C.1    Kidwell, M.G.2
  • 38
    • 0029100727 scopus 로고
    • Phylogenetic test of the molecular clock and linearized trees
    • Takezaki, N., A. Rzhetsky, and M. Nei. 1995. Phylogenetic test of the molecular clock and linearized trees. Mol. Biol. Evol. 12:823-833.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 823-833
    • Takezaki, N.1    Rzhetsky, A.2    Nei, M.3
  • 39
    • 0036790028 scopus 로고    scopus 로고
    • Evolutionary distance estimation under heterogeneous substitution pattern among lineages
    • Tamura, K., and S. Kumar. 2002. Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Mol. Biol. Evol. 19:1727-1736.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 1727-1736
    • Tamura, K.1    Kumar, S.2
  • 40
    • 0027157960 scopus 로고
    • Estimation of the number of nucleotide substitutions in the control region of mitochondrial-DNA in humans and chimpanzees
    • Tamura, K., and M. Nei. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial-DNA in humans and chimpanzees. Mol. Biol. Evol. 10:512-526.
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 512-526
    • Tamura, K.1    Nei, M.2
  • 41
    • 0001975715 scopus 로고
    • Origin of Hawaiian drosophilids inferred from alcohol dehydrogenase gene sequences
    • M. Nei and N. Takahata, eds. The Pennsylvania State University, USA, Graduate School for Advanced Studies, Hayama, Japan
    • Tamura, K., G. Toba, J. Park, and T. Aotsuka. 1995. Origin of Hawaiian drosophilids inferred from alcohol dehydrogenase gene sequences, Pp. 9-18 in M. Nei and N. Takahata, eds. Current topics on molecular evolution: proceedings of the US-Japan workshop. The Pennsylvania State University, USA, Graduate School for Advanced Studies, Hayama, Japan.
    • (1995) Current Topics on Molecular Evolution: Proceedings of the US-Japan Workshop , pp. 9-18
    • Tamura, K.1    Toba, G.2    Park, J.3    Aotsuka, T.4
  • 42
  • 43
    • 0034907353 scopus 로고    scopus 로고
    • Ddc and amd sequences resolve phylogenetic relationships of Drosophila
    • Tatarenkov, A., M. Zurovcova, and F. J. Ayala. 2001. Ddc and amd sequences resolve phylogenetic relationships of Drosophila. Mol. Phylogenet. Evol. 20:321-325.
    • (2001) Mol. Phylogenet. Evol. , vol.20 , pp. 321-325
    • Tatarenkov, A.1    Zurovcova, M.2    Ayala, F.J.3
  • 44
    • 0027521074 scopus 로고
    • Phylogenetic relationships in Drosophila: A conflict between molecular and morphological data
    • Thomas, R. H., and J. A. Hunt. 1993. Phylogenetic relationships in Drosophila: a conflict between molecular and morphological data. Mol. Biol. Evol. 10:362-374.
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 362-374
    • Thomas, R.H.1    Hunt, J.A.2
  • 45
    • 0027968068 scopus 로고
    • Clustal-W-improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. Clustal-W-improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 46
    • 0000453649 scopus 로고
    • The phylogeny, ecology, and geography of Drosophila
    • R. C. King, ed. Plenum Press, New York
    • Throckmorton, L. H. 1975. The phylogeny, ecology, and geography of Drosophila. Pp. 421-469 in R. C. King, ed. Handbook of genetics. Plenum Press, New York.
    • (1975) Handbook of Genetics , pp. 421-469
    • Throckmorton, L.H.1
  • 47
    • 0030969134 scopus 로고    scopus 로고
    • Positive selection and the molecular evolution of a gene of male reproduction, Acp26Aa of Drosophila
    • Tsaur, S. C., and C. I. Wu. 1997. Positive selection and the molecular evolution of a gene of male reproduction, Acp26Aa of Drosophila. Mol. Biol. Evol. 14:544-549.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 544-549
    • Tsaur, S.C.1    Wu, C.I.2
  • 48
    • 1242291032 scopus 로고
    • The measurement of geological time I
    • Wallace, A. R. 1870a. The measurement of geological time I. Nature 1:399-401.
    • (1870) Nature , vol.1 , pp. 399-401
    • Wallace, A.R.1
  • 49
    • 1242335950 scopus 로고
    • The measurement of geological time II
    • Wallace, A. R. 1870b. The measurement of geological time II. Nature 1:425-455.
    • (1870) Nature , vol.1 , pp. 425-455
    • Wallace, A.R.1
  • 50
    • 0025318864 scopus 로고
    • The "effective number of codons" used in a gene
    • Wright, F. 1990. The "effective number of codons" used in a gene. Gene 87:23-29.
    • (1990) Gene , vol.87 , pp. 23-29
    • Wright, F.1
  • 51
    • 0000378875 scopus 로고
    • Evidence for higher rates of nucleotide substitution in rodents than in man
    • Wu, C. I., and W. H. Li. 1985. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl. Acad. Sci. USA 82:1741-1745.
    • (1985) Proc. Natl. Acad. Sci. USA , vol.82 , pp. 1741-1745
    • Wu, C.I.1    Li, W.H.2
  • 52
    • 0035957736 scopus 로고    scopus 로고
    • Trends, rhythms, and aberrations in global climate 65 Ma to present
    • Zachos, J., M. Pagani, L. Sloan, E. Thomas, and K. Billups. 2001. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292:686-693.
    • (2001) Science , vol.292 , pp. 686-693
    • Zachos, J.1    Pagani, M.2    Sloan, L.3    Thomas, E.4    Billups, K.5


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