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Volumn 333, Issue SUPPL., 2004, Pages 81-90

Adaptive evolution and functional divergence of pepsin gene family

Author keywords

Adaptive evolution; Functional divergence; Gene duplication; Gene families; Maximum likelihood analysis; nearest neighbor interchange; NNI; Pepsins; Phylogeny; Reconciled tree; Relative rate ratio; SPR; TBR; tree bisection reconnection

Indexed keywords

PEPSIN A;

EID: 2942558757     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2004.02.011     Document Type: Article
Times cited : (40)

References (43)
  • 2
    • 0035061474 scopus 로고    scopus 로고
    • Positive and negative selection in the DAZ gene family
    • Bielawski J.P., Yang Z. Positive and negative selection in the DAZ gene family. Mol. Biol. Evol. 18:2000;523-528
    • (2000) Mol. Biol. Evol. , vol.18 , pp. 523-528
    • Bielawski, J.P.1    Yang, Z.2
  • 3
    • 0037270595 scopus 로고    scopus 로고
    • Maximum likelihood methods for detecting adaptive evolution after gene duplication
    • Bielawski J.P., Yang Z. Maximum likelihood methods for detecting adaptive evolution after gene duplication. J. Struct. Funct. Genomics. 3:2003;201-212
    • (2003) J. Struct. Funct. Genomics , vol.3 , pp. 201-212
    • Bielawski, J.P.1    Yang, Z.2
  • 4
    • 0003050642 scopus 로고
    • Estimating the inter-relationships of tetrapod groups on the basis of molecular sequence data
    • M.J. Benton. Oxford: Clarendon
    • Bishop M.J., Friday A.E. Estimating the inter-relationships of tetrapod groups on the basis of molecular sequence data. Benton M.J. The Phylogeny and Classification of the Tetrapods. 1988;33-58 Clarendon, Oxford
    • (1988) The Phylogeny and Classification of the Tetrapods , pp. 33-58
    • Bishop, M.J.1    Friday, A.E.2
  • 5
    • 43949160320 scopus 로고
    • Branch support and tree stability
    • Bremer K. Branch support and tree stability. Cladistics. 10:1994;295-304
    • (1994) Cladistics , vol.10 , pp. 295-304
    • Bremer, K.1
  • 7
    • 0037202384 scopus 로고    scopus 로고
    • An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequences
    • Creevey C., McInerney J.O. An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequences. Gene. 300:2002;43-51
    • (2002) Gene , vol.300 , pp. 43-51
    • Creevey, C.1    McInerney, J.O.2
  • 8
    • 0141626870 scopus 로고    scopus 로고
    • CRANN: Detecting adaptive evolution in protein-coding DNA sequences
    • Creevey C., McInerney J.O. CRANN: detecting adaptive evolution in protein-coding DNA sequences. Bioinformatics. 19:2003;1726
    • (2003) Bioinformatics , vol.19 , pp. 1726
    • Creevey, C.1    McInerney, J.O.2
  • 9
    • 0025290527 scopus 로고
    • The structure and function of the aspartic proteinases
    • Davies D.R. The structure and function of the aspartic proteinases. Annu. Rev. Biophys. Chem. 19:1990;189-215
    • (1990) Annu. Rev. Biophys. Chem. , vol.19 , pp. 189-215
    • Davies, D.R.1
  • 12
    • 0032728408 scopus 로고    scopus 로고
    • Statistical methods for testing functional divergence after gene duplication
    • Gu X. Statistical methods for testing functional divergence after gene duplication. Mol. Biol. Evol. 16:1999;1664-1674
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1664-1674
    • Gu, X.1
  • 13
    • 0035211809 scopus 로고    scopus 로고
    • A site-specific measure for rate difference after gene duplication and speciation
    • Gu X. A site-specific measure for rate difference after gene duplication and speciation. Mol. Bio. Evol. 18:2001;2327-2330
    • (2001) Mol. Bio. Evol. , vol.18 , pp. 2327-2330
    • Gu, X.1
  • 14
    • 0036107253 scopus 로고    scopus 로고
    • Evolutionary analysis for functional divergence of Jak protein kinase domains and tissue-specific genes
    • Gu J., Wang Y., Gu X. Evolutionary analysis for functional divergence of Jak protein kinase domains and tissue-specific genes. J. Mol. Evol. 54:2002;725-733
    • (2002) J. Mol. Evol. , vol.54 , pp. 725-733
    • Gu, J.1    Wang, Y.2    Gu, X.3
  • 15
    • 0031678692 scopus 로고    scopus 로고
    • SplitsTree: Analyzing and visualizing evolutionary data
    • Huson D.H. SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics. 14:1998;68-73
    • (1998) Bioinformatics , vol.14 , pp. 68-73
    • Huson, D.H.1
  • 16
    • 0034033897 scopus 로고    scopus 로고
    • New world monkey pepsinogens a and C, and prochymosins: Purification, characterization of enzymatic properties, cDNA cloning, and molecular evolution
    • Kageyama T. New world monkey pepsinogens A and C, and prochymosins: purification, characterization of enzymatic properties, cDNA cloning, and molecular evolution. J. Biochem. 127:2000;761-770
    • (2000) J. Biochem. , vol.127 , pp. 761-770
    • Kageyama, T.1
  • 17
    • 0036181085 scopus 로고    scopus 로고
    • Pepsinogen, progastricsin, and prochymosin: Structure, function, evolution, and development
    • Kageyama T. Pepsinogen, progastricsin, and prochymosin: structure, function, evolution, and development. CMLS, Cell. Mol. Life Sci. 59:2002;288-306
    • (2002) CMLS, Cell. Mol. Life Sci. , vol.59 , pp. 288-306
    • Kageyama, T.1
  • 18
    • 0036139211 scopus 로고    scopus 로고
    • MEGA2: Molecular evolutionary genetics analysis software
    • Kumar S., Tamura K., Jakobsen I.B., Nei M. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics. 17:2001;1244-1245
    • (2001) Bioinformatics , vol.17 , pp. 1244-1245
    • Kumar, S.1    Tamura, K.2    Jakobsen, I.B.3    Nei, M.4
  • 20
    • 0034634395 scopus 로고    scopus 로고
    • The evolutionary fate and consequences of duplicate genes
    • Lynch M., Conery J.S. The evolutionary fate and consequences of duplicate genes. Science. 290:2000;1151-1155
    • (2000) Science , vol.290 , pp. 1151-1155
    • Lynch, M.1    Conery, J.S.2
  • 21
    • 0033972072 scopus 로고    scopus 로고
    • The probability of duplicate genes preservation by subfunctionalization
    • Lynch M., Force A. The probability of duplicate genes preservation by subfunctionalization. Genetics. 154:2000;459-473
    • (2000) Genetics , vol.154 , pp. 459-473
    • Lynch, M.1    Force, A.2
  • 22
    • 0035697435 scopus 로고    scopus 로고
    • The probability of preservation of a newly arisen gene duplicate
    • Lynch M., O'Hely M., Walsh B., Force A. The probability of preservation of a newly arisen gene duplicate. Genetics. 159:2001;1789-1804
    • (2001) Genetics , vol.159 , pp. 1789-1804
    • Lynch, M.1    O'Hely, M.2    Walsh, B.3    Force, A.4
  • 23
    • 0026428610 scopus 로고
    • Adaptive protein evolution at the Adh locus in Drosophila
    • MacDonald J.H., Kreitman M. Adaptive protein evolution at the Adh locus in Drosophila. Nature. 351:1991;652-654
    • (1991) Nature , vol.351 , pp. 652-654
    • MacDonald, J.H.1    Kreitman, M.2
  • 26
    • 0023691427 scopus 로고
    • Evolution by gene duplication and compensatory advantageous mutations
    • Ohta T. Evolution by gene duplication and compensatory advantageous mutations. Genetics. 120:1988;841-847
    • (1988) Genetics , vol.120 , pp. 841-847
    • Ohta, T.1
  • 27
    • 0024356364 scopus 로고
    • Role of gene duplication in evolution
    • Ohta T. Role of gene duplication in evolution. Genome. 31:1989;304-310
    • (1989) Genome , vol.31 , pp. 304-310
    • Ohta, T.1
  • 28
    • 0021767550 scopus 로고
    • The active site of aspartic proteinases
    • Pearl L., Blundell T. The active site of aspartic proteinases. FEBS Lett. 174:1984;96-101
    • (1984) FEBS Lett. , vol.174 , pp. 96-101
    • Pearl, L.1    Blundell, T.2
  • 29
    • 0031773680 scopus 로고    scopus 로고
    • Modeltest: Testing the model of DNA substitution
    • Posada D., Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics. 14:1998;817-818
    • (1998) Bioinformatics , vol.14 , pp. 817-818
    • Posada, D.1    Crandall, K.A.2
  • 30
    • 0034736582 scopus 로고    scopus 로고
    • Sex- and tissue-specific expression of aspartic proteinases in Danio rerio (zebrafish)
    • Riggio M., Scudiero R., Filosa S., Parisi E. Sex- and tissue-specific expression of aspartic proteinases in Danio rerio (zebrafish). Gene. 260:2000;67-75
    • (2000) Gene , vol.260 , pp. 67-75
    • Riggio, M.1    Scudiero, R.2    Filosa, S.3    Parisi, E.4
  • 31
    • 0037036926 scopus 로고    scopus 로고
    • Oestrogen-induced expression of a novel liver-specific aspartic proteinase in Danio rerio (zebrafish)
    • Riggio M., Scudiero R., Filosa S., Parisi E. Oestrogen-induced expression of a novel liver-specific aspartic proteinase in Danio rerio (zebrafish). Gene. 295:2002;241-246
    • (2002) Gene , vol.295 , pp. 241-246
    • Riggio, M.1    Scudiero, R.2    Filosa, S.3    Parisi, E.4
  • 32
    • 0034129663 scopus 로고    scopus 로고
    • RR-Tree: Relative-rate tests between groups of sequences on a phylogenetic tree
    • Robinson-Rechavi M., Huchon D. RR-Tree: relative-rate tests between groups of sequences on a phylogenetic tree. Bioinformatics. 16:2000;296-297
    • (2000) Bioinformatics , vol.16 , pp. 296-297
    • Robinson-Rechavi, M.1    Huchon, D.2
  • 33
    • 0033507441 scopus 로고    scopus 로고
    • Eosinophils, ribonucleases and host defense solving the puzzle
    • Rosenberg H.F., Domachowske J.B. Eosinophils, ribonucleases and host defense solving the puzzle. Immunol. Res. 20:1999;261-274
    • (1999) Immunol. Res. , vol.20 , pp. 261-274
    • Rosenberg, H.F.1    Domachowske, J.B.2
  • 34
    • 0033973008 scopus 로고    scopus 로고
    • Tissue-specific regulation of metallothionein and metallothionein mRNA accumulation in the Antarctic notothenioid, Nototheinia coriiceps
    • Scudiero R., Verde C., Carginale V., Kille P., Capasso C., di Prisco G., Parisi E. Tissue-specific regulation of metallothionein and metallothionein mRNA accumulation in the Antarctic notothenioid, Nototheinia coriiceps. Polar Biol. 23:2000;17-23
    • (2000) Polar Biol. , vol.23 , pp. 17-23
    • Scudiero, R.1    Verde, C.2    Carginale, V.3    Kille, P.4    Capasso, C.5    Di Prisco, G.6    Parisi, E.7
  • 35
    • 0037387451 scopus 로고    scopus 로고
    • Significantly different patterns of amino acid replacement after gene duplication as compared to after speciation
    • Seoighe C., Johnston C.R., Shields D.C. Significantly different patterns of amino acid replacement after gene duplication as compared to after speciation. Mol. Biol. Evol. 20:2003;484-490
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 484-490
    • Seoighe, C.1    Johnston, C.R.2    Shields, D.C.3
  • 36
    • 0004254209 scopus 로고    scopus 로고
    • Boston: Boston University
    • Sorenson M.D. TreeRot. 1999;Boston University, Boston
    • (1999) TreeRot
    • Sorenson, M.D.1
  • 37
    • 0029836454 scopus 로고    scopus 로고
    • Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies
    • Strimmer K., von Haeseler A. Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:1996;964-969
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 964-969
    • Strimmer, K.1    Von Haeseler, A.2
  • 39
    • 0029100727 scopus 로고
    • Phylogenetic test of the molecular clock and linearized tree
    • Takezaki N., Rzhetsky A., Nei M. Phylogenetic test of the molecular clock and linearized tree. Mol. Biol. Evol. 12:1995;823-833
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 823-833
    • Takezaki, N.1    Rzhetsky, A.2    Nei, M.3
  • 40
    • 77957014026 scopus 로고
    • Gastricsin and pepsin
    • Tang J. Gastricsin and pepsin. Methods Enzymol. 19:1970;406-421
    • (1970) Methods Enzymol. , vol.19 , pp. 406-421
    • Tang, J.1
  • 41
    • 0028893838 scopus 로고
    • How often do duplicated genes evolve new functions?
    • Walsh J.B. How often do duplicated genes evolve new functions? Genetics. 139:1995;421-428
    • (1995) Genetics , vol.139 , pp. 421-428
    • Walsh, J.B.1
  • 42
    • 0031897964 scopus 로고    scopus 로고
    • Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
    • Yang Z. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15:1998;568-573
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 568-573
    • Yang, Z.1
  • 43
    • 0031960185 scopus 로고    scopus 로고
    • Synonymous and nonsynonymous rate variation in nuclear genes of mammals
    • Yang Z., Nielsen R. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J. Mol. Evol. 46:1998;409-418
    • (1998) J. Mol. Evol. , vol.46 , pp. 409-418
    • Yang, Z.1    Nielsen, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.