메뉴 건너뛰기




Volumn 56, Issue 2, 2009, Pages

The gene evolution model and computing its associated probabilities

Author keywords

Duplication; Evolution; Gene; Loss; Phylogeny; Probability; Reconciliation

Indexed keywords

ALGORITHMIC PROBLEMS; BIRTH-DEATH PROCESS; CO-EVOLUTION; DUPLICATION; EFFICIENT ALGORITHM; EVOLUTION; EVOLUTIONARY EVENTS; FUNDAMENTAL TOOLS; GENE DUPLICATIONS; GENE EVOLUTION; GENE LOSS; GENE TREE; MAXIMUM PROBABILITY; ORTHOLOGY; PARASITE-; PHYLOGENY; POSTERIOR PROBABILITY; RECONCILIATION; TREE CONSTRUCTION;

EID: 70349414048     PISSN: 00045411     EISSN: 1557735X     Source Type: Journal    
DOI: 10.1145/1502793.1502796     Document Type: Article
Times cited : (72)

References (61)
  • 2
    • 2342651581 scopus 로고    scopus 로고
    • Bayesian gene/species tree reconciliation and orthology analysis using MCMC
    • Arvestad, L., Berglund, A.-C., Lagergren, J., and Sennblad, B. 2003. Bayesian gene/species tree reconciliation and orthology analysis using MCMC. Bioinformatics 19 Suppl 1, i7-15.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL 1 , pp. 17-15
    • Arvestad, L.1    Berglund, A.-C.2    Lagergren, J.3    Sennblad, B.4
  • 4
    • 0034767147 scopus 로고    scopus 로고
    • A linear-time algorithm for computing inversion distance between signed permutations with an experimental study
    • DOI 10.1089/106652701753216503
    • Bader, D. A., Moret,B.M., and Yan, M. 2001. A linear-time algorithm for computing inversion distance between signed permutations with an experimental study. J. Comput. Biol. 8, 5, 483-491. (Pubitemid 33044073)
    • (2001) Journal of Computational Biology , vol.8 , Issue.5 , pp. 483-491
    • Bader, D.A.1    Moret, B.M.E.2    Yan, M.3
  • 6
    • 11844251253 scopus 로고    scopus 로고
    • A very elementary presentation of the Hannenhalli-Pevzner theory
    • Bergeron, A. 2005. A very elementary presentation of the Hannenhalli-Pevzner theory. Disc. Appl. Math. 146, 2, 134-145.
    • (2005) Disc. Appl. Math , vol.146 , Issue.2 , pp. 134-145
    • Bergeron, A.1
  • 10
    • 12044249534 scopus 로고
    • Probabilities of evolutionary trees
    • BROWN, J. K. M. 1994. Probabilities of evolutionary trees. Syst. Biol. 43, 1, 78-91.
    • (1994) Syst. Biol , vol.43 , Issue.1 , pp. 78-91
    • Brown, J.K.M.1
  • 12
    • 0002721941 scopus 로고    scopus 로고
    • Sorting permutations by reversals and Eulerian cycle decompositions
    • CAPRARA, A. 1999. Sorting permutations by reversals and Eulerian cycle decompositions. SIAM J. Discrete Math 12, 1, 91-110.
    • (1999) SIAM J. Discrete Math , vol.12 , Issue.1 , pp. 91-110
    • Caprara, A.1
  • 16
    • 33745796718 scopus 로고    scopus 로고
    • A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer
    • Springer-Verlag, Berlin, Germany
    • CsÜrös,M., AND MiklÓs, I. 2006. A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer. In Lecture Notes in Computer Science. Vol.3909. Springer-Verlag, Berlin, Germany, 206-220.
    • (2006) Lecture Notes in Computer Science , vol.3909 , pp. 206-220
    • Csürös, M.1    Miklós, I.2
  • 17
    • 0042570398 scopus 로고    scopus 로고
    • The roots of phylogeny: How did Haeckel build his trees?
    • DAYRAT, B. 2003. The roots of phylogeny: How did Haeckel build his trees? Syst. Biol. 52, 4, 515-527.
    • (2003) Syst. Biol , vol.52 , Issue.4 , pp. 515-527
    • Dayrat, B.1
  • 18
    • 13244292527 scopus 로고    scopus 로고
    • Gene tree distributions under the coalescent process
    • DEGNAN,J.H.,AND SALTER, L. A. 2005. Gene tree distributions under the coalescent process. Evolu- tion 59, 1, 24-37.
    • (2005) Evolu- Tion , vol.59 , Issue.1 , pp. 24-37
    • Degnan, J.H.1    Salter, L.A.2
  • 20
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • FELSENSTEIN, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17, 6, 368-376.
    • (1981) J. Mol. Evol , vol.17 , Issue.6 , pp. 368-376
    • Felsenstein, J.1
  • 21
    • 70349928438 scopus 로고    scopus 로고
    • Inferring phylogenies. Sinauer Associates
    • FITCH, W. M. 1970. Distinguishing homologous from analogous proteins
    • FELSENSTEIN, J. 2003. Inferring phylogenies. Sinauer Associates. FITCH, W. M. 1970. Distinguishing homologous from analogous proteins. Syst. Zool. 19, 2, 99-113.
    • (2003) Syst. Zool , vol.19 , Issue.2 , pp. 99-113
    • Felsenstein, J.1
  • 22
    • 33845452848 scopus 로고    scopus 로고
    • A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis
    • FITZPATRICK, D., LOGUE, M., STAJICH,J.,AND BUTLER, G. 2006. A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol. Biol. 6, 1, 99.
    • (2006) BMC Evol. Biol , vol.6 , Issue.1 , pp. 99
    • Fitzpatrick, D.1    Logue, M.2    Stajich, J.3    Butler, G.4
  • 23
    • 23944499633 scopus 로고    scopus 로고
    • Horizontal gene transfer, genome innovation and evolution
    • G0GARTEN,J. P., AND TOWNSEND, J. P. 2005. Horizontal gene transfer, genome innovation and evolution. Nat. Rev. Micro. 3, 9, 679-687.
    • (2005) Nat. Rev. Micro , vol.3 , Issue.9 , pp. 679-687
    • Gogarten, J.P.1    Townsend, J.P.2
  • 24
    • 0000365320 scopus 로고
    • Fitting the gene lineage into its species lineage: A parsimony strategy illustrated by cladograms constructed from globin sequences
    • GOODMAN, M., CSELUSNIAK, J., M00RE,G. W., R0MER0-HERRERA,A. E., and Matsuda, G. 1979. Fitting the gene lineage into its species lineage: A parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Zool. 28, 132-168.
    • (1979) Syst. Zool , vol.28 , pp. 132-168
    • Goodman, M.1    Cselusniak, J.2    Moore, G.W.3    Romero-Herrera, A.E.4    Matsuda, G.5
  • 26
    • 23744452485 scopus 로고    scopus 로고
    • Estimating the tempo and mode of gene family evolution from comparative genomic data
    • HAHN, M. W., DE BIE, T., STAJICH, J. E., NGUYEN,C.,AND CRISTIANINI, N. 2005. Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res. 15, 8, 1153-1160.
    • (2005) Genome Res , vol.15 , Issue.8 , pp. 1153-1160
    • Hahn, M.W.1    De Bie, T.2    Stajich, J.E.3    Nguyen, C.4    Cristianini, N.5
  • 27
    • 0002856077 scopus 로고    scopus 로고
    • Transforming cabbage into turnip: Apolynomial algorithm for sorting signed permutations by reversals
    • HANNENHALLI, S., AND PEVZNER, P. A. 1999. Transforming cabbage into turnip: apolynomial algorithm for sorting signed permutations by reversals. J. ACM 46, 1-27.
    • (1999) J. ACM , vol.46 , pp. 1-27
    • Hannenhalli, S.1    Pevzner, P.A.2
  • 28
    • 0001996348 scopus 로고
    • The probabilities of rooted tree-shapes generated by random bifurcation
    • HARDING, E. F. 1971. The probabilities of rooted tree-shapes generated by random bifurcation. Adv. Appl. Prob. 3, 1, 44-77.
    • (1971) Adv. Appl. Prob , vol.3 , Issue.1 , pp. 44-77
    • Harding, E.F.1
  • 29
    • 0000424609 scopus 로고
    • Testing the constant-rate neutral allele model with protein sequence data
    • HUDSON, R. R. 1983. Testing the constant-rate neutral allele model with protein sequence data. Evolution 37, 1, 203-217.
    • (1983) Evolution , vol.37 , Issue.1 , pp. 203-217
    • Hudson, R.R.1
  • 30
    • 0030617964 scopus 로고    scopus 로고
    • Statistical tests of host-parasite cospeciation
    • HUELSENBECK,J.P., RANNALA,B., AND YANG, Z. 1997. Statistical tests of host-parasite cospeciation. Evolution 51, 2, 410-1119
    • (1997) Evolution , vol.51 , Issue.2 , pp. 410-1119
    • Huelsenbeck, J.P.1    Rannala, B.2    Yang, Z.3
  • 31
    • 0034849408 scopus 로고    scopus 로고
    • MrBayes: Bayesian inference of phylogenetic trees
    • HUELSENBECK,J.P., AND RONQUIST, F. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17, 8, 754-755.
    • (2001) Bioinformatics , vol.17 , Issue.8 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 32
    • 33645850710 scopus 로고    scopus 로고
    • Phylogenomics: The beginning of incongruence?
    • JEFFROY, O., BRINKMANN, H., DELSUC,F.,AND PHILIPPE, H. 2006. Phylogenomics: the beginning of incongruence? Trends Genet. 22, 4, 225-231.
    • (2006) Trends Genet , vol.22 , Issue.4 , pp. 225-231
    • Jeffroy, O.1    Brinkmann, H.2    Delsuc, F.3    Philippe, H.4
  • 33
    • 38249043088 scopus 로고
    • Random generation of combinatorial structures from a uniform distribution
    • JERRUM, M., VALIANT, L., AND VAZIRANI, V. 1986. Random generation of combinatorial structures from a uniform distribution. Theoret. Comput. Sci. 43, 169-188.
    • (1986) Theoret. Comput. Sci , vol.43 , pp. 169-188
    • Jerrum, M.1    Valiant, L.2    Vazirani, V.3
  • 34
    • 0002024701 scopus 로고
    • On the generalized "birth-and-death" process
    • KENDALL, D. G. 1948. On the generalized "birth-and-death" process. Ann. Math. Stat. 19, 1-15.
    • (1948) Ann. Math. Stat , vol.19 , pp. 1-15
    • Kendall, D.G.1
  • 35
    • 0032976397 scopus 로고    scopus 로고
    • Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees
    • LARGET,B., AND SIMON, D. L. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16, 6, 750-759. (Pubitemid 29260829)
    • (1999) Molecular Biology and Evolution , vol.16 , Issue.6 , pp. 750-759
    • Larget, B.1    Simon, D.L.2
  • 36
    • 34548575126 scopus 로고    scopus 로고
    • Species trees from gene trees: Reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions
    • LIU,L., AND PEARL, D. K. 2007. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol. 56, 3, 504-514.
    • (2007) Syst. Biol. , vol.56 , Issue.3 , pp. 504-514
    • Liu, L.1    Pearl, D.K.2
  • 37
    • 0033972072 scopus 로고    scopus 로고
    • The probability of duplicate gene preservation by subfunctionaliza-tion
    • LYNCH, M., AND FORCE, A. 2000. The probability of duplicate gene preservation by subfunctionaliza-tion. Genetics 154, 1, 459-473.
    • (2000) Genetics , vol.154 , Issue.1 , pp. 459-473
    • Lynch, M.1    Force, A.2
  • 38
    • 2942622384 scopus 로고    scopus 로고
    • Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes
    • MIRKIN, B. G., FENNER,T.I., GALPERIN,M.Y., AND KOONIN, E. V. 2003. Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol. Biol. 3,2.
    • (2003) BMC Evol. Biol. , vol.3 , pp. 2
    • Mirkin, B.G.1    Fennert, I.2    Galperinm, Y.3    Koonin, E.V.4
  • 42
    • 12044253257 scopus 로고
    • Maps between trees and cladistic-analysis of historical associations among genes, organisms, and areas
    • PAGE, R. D. M. 1994. Maps between trees and cladistic-analysis of historical associations among genes, organisms, and areas. Syst. Biol. 43, 1, 58-77.
    • (1994) Syst. Biol. , vol.43 , Issue.1 , pp. 58-77
    • Page, R.D.M.1
  • 43
    • 0031110886 scopus 로고    scopus 로고
    • From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem
    • PAGE,R.D., AND CHARLESTON, M. A. 1997. From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Mol. Phylogenet. Evol. 7, 2, 231-240.
    • (1997) Mol. Phylogenet. Evol. , vol.7 , Issue.2 , pp. 231-240
    • Page, R.D.1    Charleston, M.A.2
  • 44
    • 0036365666 scopus 로고    scopus 로고
    • Vertebrate phylogenomics: Reconciled trees and gene duplications
    • World Scientific Publishing
    • PAGE,R.D., AND COTTON, J. A. 2002. Vertebrate phylogenomics: reconciled trees and gene duplications. In BIOCOMPUTING 2002: Proceedings of the Pacific Symposium. World Scientific Publishing, 536-547
    • (2002) BIOCOMPUTING 2002: Proceedings of the Pacific Symposium , pp. 536-547
    • Page, R.D.1    Cotton, J.A.2
  • 45
    • 0023822631 scopus 로고
    • Relationships between gene trees and species trees
    • PAMILO,P., AND NEI, M. 1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5, 5, 568-583
    • (1988) Mol. Biol. Evol. , vol.5 , Issue.5 , pp. 568-583
    • Pamilo, P.1    Nei, M.2
  • 46
    • 33646001426 scopus 로고    scopus 로고
    • Graph theoretical insights into evolution of multidomain proteins
    • PRZYTYCKA, T., DAVIS, G., SONG, N., AND DURAND, D. 2006. Graph theoretical insights into evolution of multidomain proteins. J. Comput. Biol. 13, 2, 351-363.
    • (2006) J. Comput. Biol. , vol.13 , Issue.2 , pp. 351-363
    • Przytycka, T.1    Davis, G.2    Song, N.3    Durand, D.4
  • 47
    • 0041817551 scopus 로고    scopus 로고
    • Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci
    • RANNALA,B., AND YANG, Z. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164, 4, 1645-1656.
    • (2003) Genetics , vol.164 , Issue.4 , pp. 1645-1656
    • Rannala, B.1    Yang, Z.2
  • 48
    • 0035861990 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and in- paralogs from pairwise species comparisons
    • REMM, M., STORM,C.E., AND SONNHAMMER, E. L. 2001. Automatic clustering of orthologs and in- paralogs from pairwise species comparisons. J. Mol. Biol. 314, 5, 1041-1052.
    • (2001) J. Mol. Biol. , vol.314 , Issue.5 , pp. 1041-1052
    • Remm, M.1    Stormc, E.2    Sonnhammer, E.L.3
  • 49
    • 21244454411 scopus 로고    scopus 로고
    • Explosive lineage-specific expansion of the orphan nuclear receptor HNF4 in nematodes
    • ROBINSON-RECHAVI, M., MAINA,C.V., GISSENDANNER, C. R., LAUDET,V., and SLUDER, A. 2005. Explosive lineage-specific expansion of the orphan nuclear receptor HNF4 in nematodes. J. Mol. Evol. 60, 5, 577-586.
    • (2005) J. Mol. Evol. , vol.60 , Issue.5 , pp. 577-586
    • Robinson-Rechavi, M.1    Mainac, V.2    Gissendanner, C.R.3    Laudet, V.4    Sluder, A.5
  • 50
    • 0242365676 scopus 로고    scopus 로고
    • Genome-scale approaches to resolving incongruence in molecular phylogenies
    • Rokas, A., Williams, B. L., King, N., and Carroll, S. B. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425, 6960, 798-804.
    • (2003) Nature , vol.425 , Issue.6960 , pp. 798-804
    • Rokas, A.1    Williams, B.L.2    King, N.3    Carroll, S.B.4
  • 51
    • 0036173130 scopus 로고    scopus 로고
    • Automated ortholog inference from phylogenetic trees and calculation of orthology reliability
    • STORM,C.E., AND SONNHAMMER, E. L. 2002. Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics 18, 1, 92-99
    • (2002) Bioinformatics , vol.18 , Issue.1 , pp. 92-99
    • Storm, C.E.1    Sonnhammer, E.L.2
  • 52
    • 0142028973 scopus 로고    scopus 로고
    • Comprehensive analysis of orthologous protein domains using the HOPS database
    • STORM,C. E., AND SONNHAMMER, E. L. 2003. Comprehensive analysis of orthologous protein domains using the HOPS database. Genome Res. 13, 10, 2353-2362.
    • (2003) Genome Res. , vol.13 , Issue.10 , pp. 2353-2362
    • Stormc, E.1    Sonnhammer, E.L.2
  • 53
    • 0037058983 scopus 로고    scopus 로고
    • Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics
    • SUZUKI, Y., GLAZKO,G.V., AND NEI, M. 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Nat. Acad. Sci. 99, 25, 16138-16143.
    • (2002) Proc. Nat. Acad. Sci. , vol.99 , Issue.25 , pp. 16138-16143
    • Suzuki, Y.1    Glazkog, V.2    Nei, M.3
  • 54
    • 0035002528 scopus 로고    scopus 로고
    • Nothofagus biogeography revisited with special emphasis on the enigmatic distribution of subgenus Brassospora in New Caledonia
    • SWENSON, U., BACKLUND, A., MCLOUGHLIN, S., AND HILL, R. S. 2001. Nothofagus biogeography revisited with special emphasis on the enigmatic distribution of subgenus Brassospora in New Caledonia. Cladistics 17, 1, 28-47.
    • (2001) Cladistics , vol.17 , Issue.1 , pp. 28-47
    • Swenson, U.1    Backlund, A.2    McLoughlin, S.3    Hill, R.S.4
  • 55
    • 0021066244 scopus 로고
    • Evolutionary relationship of DNA sequences in finite populations
    • TAJIMA, F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105, 2, 437-460.
    • (1983) Genetics , vol.105 , Issue.2 , pp. 437-460
    • Tajima, F.1
  • 57
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • Oct
    • TATUSOV, R. L., KoONIN,E.V., AND LIPMAN, D. J. 1997. A genomic perspective on protein families. Science 278, 5338 (Oct), 631-637.
    • (1997) Science , vol.278 , Issue.5338 , pp. 631-637
    • Tatusov, R.L.1    Koonine, V.2    Lipman, D.J.3
  • 59
    • 0030749810 scopus 로고    scopus 로고
    • Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method
    • YANG,Z., AND RANNALA, B. 1997. Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method. Mol. Biol. Evol. 14, 7, 717-724.
    • (1997) Mol. Biol. Evol , vol.14 , Issue.7 , pp. 717-724
    • Yang, Z.1    Rannala, B.2
  • 60
    • 0031876458 scopus 로고    scopus 로고
    • Towards detection of orthologues in sequence databases
    • YUAN,Y. P., EULENSTEIN, O., VlNGRON,M., AND Bork, P. 1998. Towards detection of orthologues in sequence databases. Bioinformatics 14, 3, 285-289.
    • (1998) Bioinformatics , vol.14 , Issue.3 , pp. 285-289
    • Yuany, P.1    Eulenstein, O.2    Vlngron, M.3    Bork, P.4
  • 61
    • 0013017592 scopus 로고    scopus 로고
    • RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs
    • ZMASEK,C.M., AND EDDY, S. R. 2002. RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics 3, 1, 14.
    • (2002) BMC Bioinformatics , vol.3 , Issue.1 , pp. 14
    • Zmasek, C.M.1    Eddy, S.R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.