메뉴 건너뛰기




Volumn 6, Issue , 2006, Pages

The shape of human gene family phylogenies

Author keywords

[No Author keywords available]

Indexed keywords

OPSIN; RHODOPSIN;

EID: 33750250388     PISSN: 14712148     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-6-66     Document Type: Article
Times cited : (5)

References (47)
  • 2
    • 19944362816 scopus 로고    scopus 로고
    • Analytical methods for detecting paralogy in molecular datasets
    • Cotton JA: Analytical methods for detecting paralogy in molecular datasets. Methods Enzymol 2005, 395:700-724.
    • (2005) Methods Enzymol , vol.395 , pp. 700-724
    • Cotton, J.A.1
  • 3
    • 0036213859 scopus 로고    scopus 로고
    • Evidence of gene conversion events between paralogous sequences produced by tetraploidization in salmoninae fish
    • Angers B, Gharbi K, Estoup A: Evidence of gene conversion events between paralogous sequences produced by tetraploidization in salmoninae fish. J Mol Evol 2002, 54:501-10.
    • (2002) J Mol Evol , vol.54 , pp. 501-510
    • Angers, B.1    Gharbi, K.2    Estoup, A.3
  • 4
    • 19644386079 scopus 로고    scopus 로고
    • Rates and patterns of gene duplication and loss in the human genome
    • Cotton JA, Page RDM: Rates and patterns of gene duplication and loss in the human genome. Proc R Soc Lond, Ser B 2005, 272:277-283.
    • (2005) Proc R Soc Lond, Ser B , vol.272 , pp. 277-283
    • Cotton, J.A.1    Page, R.D.M.2
  • 5
    • 0036365666 scopus 로고    scopus 로고
    • Vertebrate phylogenomics: Reconciled trees and gene duplications
    • Page RDM, Cotton JA: Vertebrate phylogenomics: reconciled trees and gene duplications. Pac Symp Biocomput 2002:536-47.
    • (2002) Pac Symp Biocomput , pp. 536-547
    • Page, R.D.M.1    Cotton, J.A.2
  • 6
    • 0002638760 scopus 로고    scopus 로고
    • Inferring evolutionary process from phylogenetic tree shape
    • Mooers AØ, Heard SB: Inferring evolutionary process from phylogenetic tree shape. Q Rev Biol 1997, 72:31-54.
    • (1997) Q Rev Biol , vol.72 , pp. 31-54
    • Mooers, A.Ø.1    Heard, S.B.2
  • 7
    • 0001778604 scopus 로고
    • A mathematical theory of evolution, based on the conclusions of Dr J. C. Willis
    • Yule GU: A mathematical theory of evolution, based on the conclusions of Dr J. C. Willis. Philos Trans R Soc Lond, Ser A 1924, 213:21-87.
    • (1924) Philos Trans R Soc Lond, Ser A , vol.213 , pp. 21-87
    • Yule, G.U.1
  • 8
    • 33747594798 scopus 로고
    • Vicariant patterns and historical explanation in biogeography
    • Rosen DE: Vicariant patterns and historical explanation in biogeography. Syst Zool 1978, 27:159-188.
    • (1978) Syst Zool , vol.27 , pp. 159-188
    • Rosen, D.E.1
  • 9
    • 0035084255 scopus 로고    scopus 로고
    • Properties of phylogenetic trees generated by Yule-type speciation models
    • McKenzie A, Steel M: Properties of phylogenetic trees generated by Yule-type speciation models. Math Biosci 2001, 170:91-112.
    • (2001) Math Biosci , vol.170 , pp. 91-112
    • McKenzie, A.1    Steel, M.2
  • 10
    • 0028873765 scopus 로고
    • Tree balance and tree completeness
    • Mooers AØ: Tree balance and tree completeness. Evolution 1995, 49:379-384.
    • (1995) Evolution , vol.49 , pp. 379-384
    • Mooers, A.Ø.1
  • 11
    • 0029821511 scopus 로고    scopus 로고
    • Do phylogenetic methods produce trees with biased shapes?
    • Huelsenbeck JP, Kirkpatrick M: Do phylogenetic methods produce trees with biased shapes? Evolution 1996, 50:1418-1424.
    • (1996) Evolution , vol.50 , pp. 1418-1424
    • Huelsenbeck, J.P.1    Kirkpatrick, M.2
  • 12
    • 0030328210 scopus 로고    scopus 로고
    • Imperfect information and the balance of cladograms and phenograms
    • Heard SB, Mooers AØ: Imperfect information and the balance of cladograms and phenograms. Syst Biol 1996, 45:115-118.
    • (1996) Syst Biol , vol.45 , pp. 115-118
    • Heard, S.B.1    Mooers, A.Ø.2
  • 13
    • 0000373233 scopus 로고
    • Comparison of observed phyogenetic topologies with null expectations among three monophyletic lineages
    • Guyer C, Slowinski JB: Comparison of observed phyogenetic topologies with null expectations among three monophyletic lineages. Evolution 1991, 45:340-350.
    • (1991) Evolution , vol.45 , pp. 340-350
    • Guyer, C.1    Slowinski, J.B.2
  • 14
    • 0030484686 scopus 로고    scopus 로고
    • Patterns in phylogenetic tree shape with variable and evolving speciation rates
    • Heard SB: Patterns in phylogenetic tree shape with variable and evolving speciation rates. Evolution 1996, 50:2141-8.
    • (1996) Evolution , vol.50 , pp. 2141-2148
    • Heard, S.B.1
  • 15
    • 33750244443 scopus 로고
    • Searching for evolutionary patterns in the shape of phylogenetic trees
    • Kirkpatrick M, Slatkin M: Searching for evolutionary patterns in the shape of phylogenetic trees. Evolution 1993, 46:1818-1826.
    • (1993) Evolution , vol.46 , pp. 1818-1826
    • Kirkpatrick, M.1    Slatkin, M.2
  • 17
    • 26444603772 scopus 로고    scopus 로고
    • Two rounds of whole genome duplication in the ancestral vertebrate
    • Dehal P, Boore JL: Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol 2005, 3:e314.
    • (2005) PLoS Biol , vol.3
    • Dehal, P.1    Boore, J.L.2
  • 18
    • 0036613237 scopus 로고    scopus 로고
    • Extensive genomic duplication during early chordate evolution
    • McLysaght A, Hokamp K, Wolfe KH: Extensive genomic duplication during early chordate evolution. Nat Genet 2002, 31:200-204.
    • (2002) Nat Genet , vol.31 , pp. 200-204
    • McLysaght, A.1    Hokamp, K.2    Wolfe, K.H.3
  • 20
    • 0028065237 scopus 로고
    • Archetypal organization of the Amphioxus Hox gene cluster
    • Garcia-Fernandez J, Holland PW: Archetypal organization of the Amphioxus Hox gene cluster. Nature 1994, 370:563-566.
    • (1994) Nature , vol.370 , pp. 563-566
    • Garcia-Fernandez, J.1    Holland, P.W.2
  • 21
  • 22
    • 0028973861 scopus 로고
    • Stumped by trees? A generalized null model for patterns of organismal diversity
    • Losos JB, Adler FR: Stumped by trees? A generalized null model for patterns of organismal diversity. Am Nat 1995, 145:329-342.
    • (1995) Am Nat , vol.145 , pp. 329-342
    • Losos, J.B.1    Adler, F.R.2
  • 24
    • 0035154891 scopus 로고    scopus 로고
    • Is tetralogy true? Lack of support for the "one-to-four rule"
    • Martin A: Is tetralogy true? lack of support for the "one-to-four rule". Mol Biol Evol 2001, 18:89-93.
    • (2001) Mol Biol Evol , vol.18 , pp. 89-93
    • Martin, A.1
  • 25
    • 0032957497 scopus 로고    scopus 로고
    • Phylogenies of developmentally important proteins do not support the hypothesis of two rounds of genome duplication early in vertebrate history
    • Hughes AL: Phylogenies of developmentally important proteins do not support the hypothesis of two rounds of genome duplication early in vertebrate history. J Mol Evol 1999, 48:565-76.
    • (1999) J Mol Evol , vol.48 , pp. 565-576
    • Hughes, A.L.1
  • 26
    • 0035865239 scopus 로고    scopus 로고
    • Evolutionary analyses of the human genome
    • Li W-H, Gu Z, Wang H, Nekrutenko A: Evolutionary analyses of the human genome. Nature 2001, 409:847-9.
    • (2001) Nature , vol.409 , pp. 847-849
    • Li, W.-H.1    Gu, Z.2    Wang, H.3    Nekrutenko, A.4
  • 28
    • 0034100582 scopus 로고    scopus 로고
    • Distributions of cherries for two models of trees
    • McKenzie A, Steel M: Distributions of cherries for two models of trees. Math Biosci 2000, 164:81-92.
    • (2000) Math Biosci , vol.164 , pp. 81-92
    • McKenzie, A.1    Steel, M.2
  • 29
    • 0035989047 scopus 로고    scopus 로고
    • Does imbalance in phylogenies reflect only bias?
    • Stam E: Does imbalance in phylogenies reflect only bias? Evolution 2002, 56:1292-1295.
    • (2002) Evolution , vol.56 , pp. 1292-1295
    • Stam, E.1
  • 32
    • 0001416546 scopus 로고
    • Patterns in tree balance among cladistic, phenetic, and randomly generated phylogenetic trees
    • Heard SB: Patterns in tree balance among cladistic, phenetic, and randomly generated phylogenetic trees. Evolution 1992, 46:1818-1826.
    • (1992) Evolution , vol.46 , pp. 1818-1826
    • Heard, S.B.1
  • 33
    • 0032516073 scopus 로고    scopus 로고
    • Extent of genomic rearrangement after genome duplication in yeast
    • Seoighe C, Wolfe KH: Extent of genomic rearrangement after genome duplication in yeast. Proc Natl Acad Sci USA 1998, 95:4447-4452.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 4447-4452
    • Seoighe, C.1    Wolfe, K.H.2
  • 34
    • 0034634395 scopus 로고    scopus 로고
    • The evolutionary fate and consequences of duplicate genes
    • Lynch M, Conery JS: The evolutionary fate and consequences of duplicate genes. Science 2000, 290:1151-5.
    • (2000) Science , vol.290 , pp. 1151-1155
    • Lynch, M.1    Conery, J.S.2
  • 35
    • 0035344021 scopus 로고    scopus 로고
    • Yesterday's polyploids and the mystery of diploidization
    • Wolfe KH: Yesterday's polyploids and the mystery of diploidization. Nat Rev Genet 2001, 2:333-41.
    • (2001) Nat Rev Genet , vol.2 , pp. 333-341
    • Wolfe, K.H.1
  • 38
    • 0035863762 scopus 로고    scopus 로고
    • The estimation of statistical parameters for local alignment score distributions
    • Altschul SF, Bundschuh R, Olsen R, Hwa T: The estimation of statistical parameters for local alignment score distributions. Nucleic Acids Res 2001, 29:351-61.
    • (2001) Nucleic Acids Res , vol.29 , pp. 351-361
    • Altschul, S.F.1    Bundschuh, R.2    Olsen, R.3    Hwa, T.4
  • 39
    • 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 JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-80.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 40
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4:406-25.
    • (1987) Mol Biol Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 41
    • 0036205377 scopus 로고    scopus 로고
    • TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
    • Schmidt HA, Strimmer K, Vingron M, von Haeseler A: 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    Von Haeseler, A.4
  • 42
    • 0002168111 scopus 로고
    • Review of Phylogenetics: The Theory and Practice of Phylogenetic Systematics
    • Colless DH: Review of Phylogenetics: the Theory and Practice of Phylogenetic Systematics. Syst Zool 1982, 31:100-104.
    • (1982) Syst Zool , vol.31 , pp. 100-104
    • Colless, D.H.1
  • 43
    • 0000555301 scopus 로고
    • Central moments and probability distribution of Colless's coefficient of tree imbalance
    • Rogers JS: Central moments and probability distribution of Colless's coefficient of tree imbalance. Evolution 1994, 48:2026-2036.
    • (1994) Evolution , vol.48 , pp. 2026-2036
    • Rogers, J.S.1
  • 44
    • 12044257887 scopus 로고
    • Response of Colless's tree imbalance to number of terminal taxa
    • Rogers JS: Response of Colless's tree imbalance to number of terminal taxa. Syst Biol 1993, 42:102-105.
    • (1993) Syst Biol , vol.42 , pp. 102-105
    • Rogers, J.S.1
  • 45
    • 0036963179 scopus 로고    scopus 로고
    • Power of Eight Tree Shape Statistics to Detect Nonrandom Diversification: A Comparison by Simulation of Two Models of Cladogenesis
    • Agapow PM, Purvis A: Power of Eight Tree Shape Statistics to Detect Nonrandom Diversification: A Comparison by Simulation of Two Models of Cladogenesis. Syst Biol 2003, 51:866-872.
    • (2003) Syst Biol , vol.51 , pp. 866-872
    • Agapow, P.M.1    Purvis, A.2
  • 46
    • 33750245951 scopus 로고    scopus 로고
    • Which random processes describe the tree of life? A large-scale study of phylogenetic tree imblance
    • Blum MGB, François O: Which random processes describe the tree of life? A large-scale study of phylogenetic tree imblance. Syst Biol 2006, 55:685-691.
    • (2006) Syst Biol , vol.55 , pp. 685-691
    • Blum, M.G.B.1    François, O.2
  • 47
    • 33750276566 scopus 로고    scopus 로고
    • The mean, variance and limiting distribution of two statistics sensitive to phylogenetic tree balance
    • in press
    • Blum MGB, François O, Janson S: The mean, variance and limiting distribution of two statistics sensitive to phylogenetic tree balance. Annals Appl Prob in press.
    • Annals Appl Prob
    • Blum, M.G.B.1    François, O.2    Janson, S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.