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Volumn 62, Issue 1, 2012, Pages 214-223

Increasing the data size to accurately reconstruct the phylogenetic relationships between nine subgroups of the Drosophila melanogaster species group (Drosophilidae, Diptera)

Author keywords

AU test; Bayesian; Maximum likelihood; Melanogaster species group; Multiple genes; Phylogeny

Indexed keywords

DROSOPHILA PROTEIN; RNA 28S;

EID: 83655167151     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2011.09.018     Document Type: Article
Times cited : (41)

References (42)
  • 1
    • 0021186493 scopus 로고
    • On the evolutionary relationships of Drosophila melanogaster
    • Ashburner M., Bodmer M., Lemeunier F. On the evolutionary relationships of Drosophila melanogaster. Dev. Genet. 1984, 4:295-312.
    • (1984) Dev. Genet. , vol.4 , pp. 295-312
    • Ashburner, M.1    Bodmer, M.2    Lemeunier, F.3
  • 2
    • 84981625657 scopus 로고
    • Current status of the Drosophila melanogaster species group (Diptera)
    • Bock I.R. Current status of the Drosophila melanogaster species group (Diptera). Syst. Entomol. 1980, 5:341-356.
    • (1980) Syst. Entomol. , vol.5 , pp. 341-356
    • Bock, I.R.1
  • 3
    • 1542347067 scopus 로고    scopus 로고
    • Neighbor-net: an agglomerative method for the construction of phylogenetic networks
    • Bryant D., Moulton V. Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol. Biol. Evol. 2004, 21:255-265.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 255-265
    • Bryant, D.1    Moulton, V.2
  • 4
    • 33846632782 scopus 로고    scopus 로고
    • A phylogeny of Drosophilidae using the Amyrel gene: questioning the Drosophila melanogaster species group boundaries
    • Da Lage J.L., Kergoat G.J., Maczkowiak F., Silvain J.-F., Cariou M.-L., Lachaise D. A phylogeny of Drosophilidae using the Amyrel gene: questioning the Drosophila melanogaster species group boundaries. J. Zool. Syst. Evol. Res. 2007, 45(1):47-63.
    • (2007) J. Zool. Syst. Evol. Res. , vol.45 , Issue.1 , pp. 47-63
    • Da Lage, J.L.1    Kergoat, G.J.2    Maczkowiak, F.3    Silvain, J.-F.4    Cariou, M.-L.5    Lachaise, D.6
  • 5
    • 34247855965 scopus 로고    scopus 로고
    • Research on the karyotype melanogaster species group and evolution of Drosophila
    • Deng Q.H., Zeng Q.T., Qian Y.H., Li C.X., Yang Y. Research on the karyotype melanogaster species group and evolution of Drosophila. J. Genet. Genom. 2007, 34(3):196-213.
    • (2007) J. Genet. Genom. , vol.34 , Issue.3 , pp. 196-213
    • Deng, Q.H.1    Zeng, Q.T.2    Qian, Y.H.3    Li, C.X.4    Yang, Y.5
  • 6
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl. Acids Res. 2004, 32:1792-1797.
    • (2004) Nucl. Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 7
    • 0000637681 scopus 로고
    • Single-fly DNA preps for PCR
    • Gloor G., Engels W. Single-fly DNA preps for PCR. Dros. Inf. Serv. 1992, 71:148-149.
    • (1992) Dros. Inf. Serv. , vol.71 , pp. 148-149
    • Gloor, G.1    Engels, W.2
  • 8
    • 0035729730 scopus 로고    scopus 로고
    • Phylogenetic utility of mitochondrial COI and COII nuclear Gpdh genes in Drosophila
    • Goto S.G., Kimura M. Phylogenetic utility of mitochondrial COI and COII nuclear Gpdh genes in Drosophila. Mol. Phylogenet. Evol. 2001, 18:404-422.
    • (2001) Mol. Phylogenet. Evol. , vol.18 , pp. 404-422
    • Goto, S.G.1    Kimura, M.2
  • 9
    • 0002433981 scopus 로고
    • A phylogenetic revised classification of genera in the Drosophilidae (Diptera)
    • Grimaldi T. A phylogenetic revised classification of genera in the Drosophilidae (Diptera). Bull. Am. Mus. Nat. Hist. 1991, 197:1-139.
    • (1991) Bull. Am. Mus. Nat. Hist. , vol.197 , pp. 1-139
    • Grimaldi, T.1
  • 10
    • 0033946523 scopus 로고    scopus 로고
    • Removal of microsatellite interruptions by DNA replication slippage: phylogenetic evidence from Drosophila
    • Harr B., Zangerl B., Schlötterer C. Removal of microsatellite interruptions by DNA replication slippage: phylogenetic evidence from Drosophila. Mol. Biol. Evol. 2000, 17:1001-1009.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1001-1009
    • Harr, B.1    Zangerl, B.2    Schlötterer, C.3
  • 11
    • 0242669921 scopus 로고    scopus 로고
    • Is sparse taxon sampling a problem for phylogenetic inference?
    • Hillis D.M., Pollock D., Mcguire J.A., Zwickl D.J. Is sparse taxon sampling a problem for phylogenetic inference?. Syst. Biol. 2003, 2(1):124-126.
    • (2003) Syst. Biol. , vol.2 , Issue.1 , pp. 124-126
    • Hillis, D.M.1    Pollock, D.2    Mcguire, J.A.3    Zwickl, D.J.4
  • 12
    • 30744470609 scopus 로고    scopus 로고
    • Application of phylogenetic networks in evolutionary studies
    • Huson D.H., Bryant D.H. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 2006, 23:254-267.
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 254-267
    • Huson, D.H.1    Bryant, D.H.2
  • 13
    • 0030802497 scopus 로고    scopus 로고
    • Molecular evolution of the amy multigenes in the subgenus of male Drosophila
    • Inomata N., Tachida H., Yamazaki T. Molecular evolution of the amy multigenes in the subgenus of male Drosophila. Mol. Biol. Evol. 1997, 14:942-950.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 942-950
    • Inomata, N.1    Tachida, H.2    Yamazaki, T.3
  • 14
    • 0345393146 scopus 로고    scopus 로고
    • Macro-evolutionary relationships of species of Drosophila melanogaster group based on mtDNA sequences
    • Kastanis P., Eliopoulos E., Goulielmos G.N., Tsakas S., Loukas M. Macro-evolutionary relationships of species of Drosophila melanogaster group based on mtDNA sequences. Mol. Phylogenet. Evol. 2003, 28(3):518-528.
    • (2003) Mol. Phylogenet. Evol. , vol.28 , Issue.3 , pp. 518-528
    • Kastanis, P.1    Eliopoulos, E.2    Goulielmos, G.N.3    Tsakas, S.4    Loukas, M.5
  • 15
    • 0036804525 scopus 로고    scopus 로고
    • Phylogeny of the oriental Drosophila melanogaster species group: a multilocus reconstruction
    • Kopp A., True J.R. Phylogeny of the oriental Drosophila melanogaster species group: a multilocus reconstruction. Syst. Biol. 2002, 51:1-20.
    • (2002) Syst. Biol. , vol.51 , pp. 1-20
    • Kopp, A.1    True, J.R.2
  • 16
    • 33646393786 scopus 로고    scopus 로고
    • Basal relationships in the Drosophila melanogaster species group
    • Kopp A. Basal relationships in the Drosophila melanogaster species group. Mol. Phylogenet. Evol. 2006, 39(3):787-798.
    • (2006) Mol. Phylogenet. Evol. , vol.39 , Issue.3 , pp. 787-798
    • Kopp, A.1
  • 17
    • 0001670506 scopus 로고
    • The melanogaster species group
    • Academic Press, New York, USA, M. Ashburner, H.L. Carson, J.N. Thompson (Eds.)
    • Lemeunier F., David J.R., Tsacas L. The melanogaster species group. Genetics and Biology of Drosophila 1986, vol. 3e:148-256. Academic Press, New York, USA. M. Ashburner, H.L. Carson, J.N. Thompson (Eds.).
    • (1986) Genetics and Biology of Drosophila , vol.3 , pp. 148-256
    • Lemeunier, F.1    David, J.R.2    Tsacas, L.3
  • 18
    • 25144466855 scopus 로고    scopus 로고
    • The phylogeny of the subgroups within the melanogaster species group: likelihood tests on COI and COII sequences and a Bayesian estimate of phylogeny
    • Lewis R.L., Beckenbach A.T., Mooers A.O. The phylogeny of the subgroups within the melanogaster species group: likelihood tests on COI and COII sequences and a Bayesian estimate of phylogeny. Mol. Phylogenet. Evol. 2005, 37:15-24.
    • (2005) Mol. Phylogenet. Evol. , vol.37 , pp. 15-24
    • Lewis, R.L.1    Beckenbach, A.T.2    Mooers, A.O.3
  • 19
    • 34247870713 scopus 로고    scopus 로고
    • Phylogeny of melanogster species group inferred from ND4L and ND4 genes
    • Mou S.L., Zeng Q.T., Yang Y., Qian Y.H., Hu G.A. Phylogeny of melanogster species group inferred from ND4L and ND4 genes. Zool. Res. 2005, 26(4):344-349.
    • (2005) Zool. Res. , vol.26 , Issue.4 , pp. 344-349
    • Mou, S.L.1    Zeng, Q.T.2    Yang, Y.3    Qian, Y.H.4    Hu, G.A.5
  • 20
    • 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., Kidwell M.G. Phylogeny of the subgenus Sophophora (Diptera: Drosophilidae) based on combined analysis of nuclear and mitochondrial sequences. Mol. Phylogenet. Evol. 2002, 22:442-453.
    • (2002) Mol. Phylogenet. Evol. , vol.22 , pp. 442-453
    • O'Grady, P.M.1    Kidwell, M.G.2
  • 21
    • 0030203863 scopus 로고    scopus 로고
    • TreeView: an application to display phylogenetic trees on personal computers
    • Page R.D. TreeView: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 1996, 12:357-358.
    • (1996) Comput. Appl. Biosci. , vol.12 , pp. 357-358
    • Page, R.D.1
  • 22
    • 0027440796 scopus 로고
    • Molecular phylogeny of Drosophila based on ribosomal RNA sequences
    • Pélandakis M., Solignac M. Molecular phylogeny of Drosophila based on ribosomal RNA sequences. J. Mol. Evol. 1993, 37:525-543.
    • (1993) J. Mol. Evol. , vol.37 , pp. 525-543
    • Pélandakis, M.1    Solignac, M.2
  • 23
    • 0036699885 scopus 로고    scopus 로고
    • Increased taxon sampling is advantageous for phylogenetic inference
    • Pollock D.D., Zwickl D.J., Mcguire J.A., Hillis D.M. Increased taxon sampling is advantageous for phylogenetic inference. Syst. Biol. 2002, 51:664-671.
    • (2002) Syst. Biol. , vol.51 , pp. 664-671
    • Pollock, D.D.1    Zwickl, D.J.2    Mcguire, J.A.3    Hillis, D.M.4
  • 24
    • 0031773680 scopus 로고    scopus 로고
    • MODELTEST: testing the model of DNA substitution
    • Posada D., Crandall K. MODELTEST: testing the model of DNA substitution. Bioinformatics 1998, 14(9):817-818.
    • (1998) Bioinformatics , vol.14 , Issue.9 , pp. 817-818
    • Posada, D.1    Crandall, K.2
  • 25
  • 26
    • 17744398025 scopus 로고    scopus 로고
    • More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy
    • Rokas A., Carroll S.B. More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol. Biol. Evol. 2005, 22:1337-1344.
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 1337-1344
    • Rokas, A.1    Carroll, S.B.2
  • 27
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: bayesian phylogenetic inference under mixed models
    • Ronquist F., Huelsenbeck J.P. MrBayes 3: bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 28
    • 0036585595 scopus 로고    scopus 로고
    • Phylogeny of a paradigm lineage: the Drosophila melanogaster species group (Diptera: Drosophilidae)
    • Schawaroch V.A. Phylogeny of a paradigm lineage: the Drosophila melanogaster species group (Diptera: Drosophilidae). Biol. J. Linn. Soc. 2002, 76(1):21-37.
    • (2002) Biol. J. Linn. Soc. , vol.76 , Issue.1 , pp. 21-37
    • Schawaroch, V.A.1
  • 29
    • 0028266426 scopus 로고
    • Comparative evolutionary analysis of rDNA ITS regions in Drosophila
    • Schlötterer C., Hauser M.T. Comparative evolutionary analysis of rDNA ITS regions in Drosophila. Mol. Biol. Evol. 1994, 11(3):513-522.
    • (1994) Mol. Biol. Evol. , vol.11 , Issue.3 , pp. 513-522
    • Schlötterer, C.1    Hauser, M.T.2
  • 30
    • 0036205377 scopus 로고    scopus 로고
    • TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing
    • Schmidt H.A., Strimmer K., Vingron M., Haeseler A.V. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 2002, 18:502-504.
    • (2002) Bioinformatics , vol.18 , pp. 502-504
    • Schmidt, H.A.1    Strimmer, K.2    Vingron, M.3    Haeseler, A.V.4
  • 31
    • 0036139287 scopus 로고    scopus 로고
    • CONSEL: for assessing the confidence of phylogenetic tree selection
    • Shimodaira H., Hasegawa M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 2001, 17:1246-1247.
    • (2001) Bioinformatics , vol.17 , pp. 1246-1247
    • Shimodaira, H.1    Hasegawa, M.2
  • 32
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 33
    • 83655165813 scopus 로고    scopus 로고
    • PAUP*: Phylogenetic Analysis Using Parsimony (* and Other Methods) Version 4. Associates, Sinauer, Sunderland, MA.
    • Swofford, D.L., 2002. PAUP*: Phylogenetic Analysis Using Parsimony (* and Other Methods) Version 4. Associates, Sinauer, Sunderland, MA.
    • (2002)
    • Swofford, D.L.1
  • 34
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    • Tamura K., Dudley J., Nei M., Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 35
    • 0033531142 scopus 로고    scopus 로고
    • Phylogenetic analysis of Euthyneura (Gastropoda) by means of the 16S rRNA gene: use of a 'fast' gene for 'higher-level' phylogenies
    • Thollesson M. Phylogenetic analysis of Euthyneura (Gastropoda) by means of the 16S rRNA gene: use of a 'fast' gene for 'higher-level' phylogenies. Proc. Roy. Soc. Lond. B 1999, 266:75-83.
    • (1999) Proc. Roy. Soc. Lond. B , vol.266 , pp. 75-83
    • Thollesson, M.1
  • 36
    • 0000453649 scopus 로고
    • The phylogeny, ecology, and geography of Drosophila
    • Plenum, New York, R.C. King (Ed.)
    • Throckmorton L.H. The phylogeny, ecology, and geography of Drosophila. Handbook of Genetics 1975, vol. 3:421-469. Plenum, New York. R.C. King (Ed.).
    • (1975) Handbook of Genetics , vol.3 , pp. 421-469
    • Throckmorton, L.H.1
  • 37
    • 67651023133 scopus 로고    scopus 로고
    • A supertree analysis and literature review of the genus Drosophila and closely related genera (Diptera, Drosophilidae)
    • Van der Linde K., Houle D. A supertree analysis and literature review of the genus Drosophila and closely related genera (Diptera, Drosophilidae). Insect. Syst. Evol. 2008, 39:241-267.
    • (2008) Insect. Syst. Evol. , vol.39 , pp. 241-267
    • Van der Linde, K.1    Houle, D.2
  • 38
  • 39
    • 34248679898 scopus 로고    scopus 로고
    • Phylogenetic incongruence in the Drosophila melanogaster species group
    • Wong A., Jensen J.D., Pool J.E., Aquadro C.F. Phylogenetic incongruence in the Drosophila melanogaster species group. Mol. Phylogenet. Evol. 2007, 43(3):1138-1150.
    • (2007) Mol. Phylogenet. Evol. , vol.43 , Issue.3 , pp. 1138-1150
    • Wong, A.1    Jensen, J.D.2    Pool, J.E.3    Aquadro, C.F.4
  • 41
    • 0842287969 scopus 로고    scopus 로고
    • Phylogenetic relationships of the Drosophila melanogaster species group deduced from spacer regions of histone gene H2A
    • Yang Y., Zhang Y.P., Qian Y.H., Zeng Q.T. Phylogenetic relationships of the Drosophila melanogaster species group deduced from spacer regions of histone gene H2A. Mol. Phylogenet. Evol. 2004, 30:336-343.
    • (2004) Mol. Phylogenet. Evol. , vol.30 , pp. 336-343
    • Yang, Y.1    Zhang, Y.P.2    Qian, Y.H.3    Zeng, Q.T.4
  • 42
    • 0036699481 scopus 로고    scopus 로고
    • Increased taxon sampling greatly reduces phylogenetic error
    • Zwickl D.J., Hillis D.M. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 2002, 51:588-598.
    • (2002) Syst. Biol. , vol.51 , pp. 588-598
    • Zwickl, D.J.1    Hillis, D.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.