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Volumn 59, Issue 6, 2010, Pages 1843-1852

The application of cophylogenic tools to gene sets

Author keywords

Cophylogeny; Evolutionary models; ParaFit; Tanglegram

Indexed keywords

DATA SET; GENE; MATHEMATICAL ANALYSIS; NUMERICAL MODEL; PHYLOGENETICS; PHYLOGENY; TAXONOMY;

EID: 78751507560     PISSN: 00400262     EISSN: None     Source Type: Journal    
DOI: 10.1002/tax.596015     Document Type: Article
Times cited : (2)

References (61)
  • 1
    • 33845904407 scopus 로고    scopus 로고
    • MtArt: A new model of amino acid replacement for Arthropoda
    • Abascal, F., Posada, D. & Zardoya, R. 2007. MtArt: A new model of amino acid replacement for Arthropoda. Molec. Biol. Evol. 24: 1-5.
    • (2007) Molec. Biol. Evol , vol.24 , pp. 1-5
    • Abascal, F.1    Posada, D.2    Zardoya, R.3
  • 2
    • 18744382506 scopus 로고    scopus 로고
    • ProtTest: Selection of best-fit models of protein evolution
    • Abascal, F., Zardoya, R. & Posada, D. 2005. ProtTest: Selection of best-fit models of protein evolution. Bioinformatics 21: 2104-2105.
    • (2005) Bioinformatics , vol.21 , pp. 2104-2105
    • Abascal, F.1    Zardoya, R.2    Posada, D.3
  • 3
    • 0036699888 scopus 로고    scopus 로고
    • The utility of the Incongruence Length Difference test
    • Barker, F.K. & Lutzoni, F.M. 2002. The utility of the Incongruence Length Difference test. Syst. Biol. 51: 625-637.
    • (2002) Syst. Biol , vol.51 , pp. 625-637
    • Barker, F.K.1    Lutzoni, F.M.2
  • 4
    • 0002844544 scopus 로고
    • Combining trees as a way of combining data set for phylogenetic inference, and the desirability of combining gene trees
    • Baum, B.R. 1992. Combining trees as a way of combining data set for phylogenetic inference, and the desirability of combining gene trees. Taxon 41: 3-10.
    • (1992) Taxon , vol.41 , pp. 3-10
    • Baum, B.R.1
  • 5
    • 77649299742 scopus 로고    scopus 로고
    • Co-dependence of repetitive sequence classes in genomes: The phylogenetic analysis of 5S rDNA families in Hordeum (Triticeae: Poaceae)
    • Baum, B.R., Edwards, T. & Johnson, D.A. 2010. Co-dependence of repetitive sequence classes in genomes: The phylogenetic analysis of 5S rDNA families in Hordeum (Triticeae: Poaceae). Genome 53: 180-202.
    • (2010) Genome , vol.53 , pp. 180-202
    • Baum, B.R.1    Edwards, T.2    Johnson, D.A.3
  • 8
    • 0029030476 scopus 로고
    • Inhibition of chloroplast DNA recombination and repair by dominant negative mutants of Escherichia coli RecA
    • Cerutti, H., Johnson, A.M., Boyton, J.E. & Gillham, N.W. 1995. Inhibition of chloroplast DNA recombination and repair by dominant negative mutants of Escherichia coli RecA. Molec. Cell. Biol. 15: 3003-3011
    • (1995) Molec. Cell. Biol , vol.15 , pp. 3003-3011
    • Cerutti, H.1    Johnson, A.M.2    Boyton, J.E.3    Gillham, N.W.4
  • 9
    • 78651307869 scopus 로고    scopus 로고
    • Principles of cophylogenetic maps
    • in: Lässig, M. & Vailleriani, A. (eds.), Berlin: Springer
    • Charleston, M.A. 2002. Principles of cophylogenetic maps. Pp. 122-147 in: Lässig, M. & Vailleriani, A. (eds.), Biological evolution and statistical physics. Berlin: Springer.
    • (2002) Biological Evolution and Statistical Physics , pp. 122-147
    • Charleston, M.A.1
  • 11
    • 0030816742 scopus 로고    scopus 로고
    • Can three incongruence tests predict when data should be combined?
    • Cunningham, C.W. 1997. Can three incongruence tests predict when data should be combined? Molec. Biol. Evol. 14: 733-740,
    • (1997) Molec. Biol. Evol , vol.14 , pp. 733-740
    • Cunningham, C.W.1
  • 12
    • 0000228203 scopus 로고
    • A model of evolutionary change in proteins
    • in: Dayhoff, M.O. (ed.), Washington, D.C.: National Biomedical Research Foundation
    • Dayhoff, M.O., Schwartz, R.M. & Orcutt, B.C. 1978. A model of evolutionary change in proteins. Pp. 345-352 in: Dayhoff, M.O. (ed.), Atlas of protein sequence and structure. Washington, D.C.: National Biomedical Research Foundation.
    • (1978) Atlas of Protein Sequence and Structure , pp. 345-352
    • Dayhoff, M.O.1    Schwartz, R.M.2    Orcutt, B.C.3
  • 13
    • 33344465800 scopus 로고    scopus 로고
    • Relaxed phylogenetics and dating
    • Doi:10.1371/journal.pbio.0040088
    • Drummond, A.J., Ho, S.Y.W., Phillips, M.J. & Rambaut, A. 2006. Relaxed phylogenetics and dating. PLoS Biol. 4: e88. Doi:10.1371/journal.pbio.0040088
    • (2006) PLoS Biol , vol.4
    • Drummond, A.J.1    Ho, S.Y.W.2    Phillips, M.J.3    Rambaut, A.4
  • 15
    • 0029068893 scopus 로고
    • Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites
    • Gu, X., Fu, Y.X. & Li, W.H. 1995. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Molec. Biol. Evol. 12: 546-557.
    • (1995) Molec. Biol. Evol , vol.12 , pp. 546-557
    • Gu, X.1    Fu, Y.X.2    Li, W.H.3
  • 16
    • 63149159234 scopus 로고    scopus 로고
    • Phylogeny, origin and biogeographic history of Aesculus L. (Sapindales) - an update from combined analysis of DNA sequences, morphology, and fossils
    • Harris, A.J., Xiang, Q.Y. & Thomas, D.T. 2009. Phylogeny, origin and biogeographic history of Aesculus L. (Sapindales) - an update from combined analysis of DNA sequences, morphology, and fossils. Taxon 58: 108-126.
    • (2009) Taxon , vol.58 , pp. 108-126
    • Harris, A.J.1    Xiang, Q.Y.2    Thomas, D.T.3
  • 17
    • 0022376704 scopus 로고
    • Dating the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa, M., Kishino, K. & Yano, T. 1985. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Molec. Evol. 22: 160-174.
    • (1985) J. Molec. Evol , vol.22 , pp. 160-174
    • Hasegawa, M.1    Kishino, K.2    Yano, T.3
  • 18
    • 77954899417 scopus 로고    scopus 로고
    • ArXiv: 0809.1908v3 [q-bio.PE], eprint service, unpaginated PDF, accessed 20 March 2010
    • Huggins, P., Owen, M. & Yoshida, R. 2009. First steps toward the geometry of cophylogeny. ArXiv: 0809.1908v3 [q-bio.PE], eprint service, unpaginated PDF, available at http://arxiv.org/abs/0809.1908v3 (accessed 20 March 2010).
    • (2009) First Steps Toward the Geometry of Cophylogeny
    • Huggins, P.1    Owen, M.2    Yoshida, R.3
  • 19
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones, D.T., Taylor, W.R. & Thornton, J.M. 1992. The rapid generation of mutation data matrices from protein sequences. Computer Appl. Biosci. 8: 275-282.
    • (1992) Computer Appl. Biosci , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 20
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • in: Munro, H.N. (ed.), New York: Academic Press
    • Jukes, T.H. & Cantor, C.R. 1969. Evolution of protein molecules. Pp. 21-132 in: Munro, H.N. (ed.), Mammalian protein metabolism. New York: Academic Press.
    • (1969) Mammalian Protein Metabolism , pp. 21-132
    • Jukes, T.H.1    Cantor, C.R.2
  • 21
    • 0030425120 scopus 로고    scopus 로고
    • When genes tell different stories: The diploid genera of the Triticeae (Gramineae)
    • Kellogg, E.A., Appels, R. & Mason-Gamer, R.J. 1996. When genes tell different stories: The diploid genera of the Triticeae (Gramineae). Syst. Bot. 21: 321-347.
    • (1996) Syst. Bot , vol.21 , pp. 321-347
    • Kellogg, E.A.1    Appels, R.2    Mason-Gamer, R.J.3
  • 22
    • 51549083858 scopus 로고    scopus 로고
    • Incongruence between cpDNA and nrITS trees indicates extensive hybridization within Eupersicaria (Polygonaceae)
    • Kim, S.T. & Donoghue, M.J. 2008. Incongruence between cpDNA and nrITS trees indicates extensive hybridization within Eupersicaria (Polygonaceae). Amer. J. Bot. 95: 112-1135.
    • (2008) Amer. J. Bot , vol.95 , pp. 112-1135
    • Kim, S.T.1    Donoghue, M.J.2
  • 23
    • 2942525509 scopus 로고    scopus 로고
    • On total evidence: For the re cord
    • Kluge, A. 2004. On total evidence: For the re cord. Cladistics 20: 205-207.
    • (2004) Cladistics , vol.20 , pp. 205-207
    • Kluge, A.1
  • 24
    • 0033367329 scopus 로고    scopus 로고
    • Mitochondrial genome evolution and the origin of eukaryotes
    • Lang, B.F., Gray, M.W. & Burger, G. 1999. Mitochondrial genome evolution and the origin of eukaryotes. Annual Rev. Genet. 33: 351-97.
    • (1999) Annual Rev. Genet , vol.33 , pp. 351-397
    • Lang, B.F.1    Gray, M.W.2    Burger, G.3
  • 26
    • 0036554493 scopus 로고    scopus 로고
    • A statistical test for host-parasite coevolution
    • Legendre, P., Desdevises, Y. & Bazin, E. 2002. A statistical test for host-parasite coevolution. Syst. Biol. 51: 217-234.
    • (2002) Syst. Biol , vol.51 , pp. 217-234
    • Legendre, P.1    Desdevises, Y.2    Bazin, E.3
  • 28
    • 54949090066 scopus 로고    scopus 로고
    • BEST: Bayesian estimation of species trees under the coalescent model
    • Liu, L. 2008. BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics 24: 2542-2543.
    • (2008) Bioinformatics , vol.24 , pp. 2542-2543
    • Liu, L.1
  • 29
    • 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. & 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: 504-514.
    • (2007) Syst. Biol , vol.56 , pp. 504-514
    • Liu, L.1    Pearl, D.K.2
  • 31
    • 33644606488 scopus 로고    scopus 로고
    • Inferring phylogeny despite incomplete lineage sorting
    • Maddison, W.P. & Knowles, L.L. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 58: 21-30.
    • (2006) Syst. Biol , vol.58 , pp. 21-30
    • Maddison, W.P.1    Knowles, L.L.2
  • 32
    • 24644519796 scopus 로고    scopus 로고
    • Angiosperm divergencetimes: The effect of genes, codon positions, and time constraints
    • Magallón, S.A. & Sanderson, M.J. 2005. Angiosperm divergencetimes: The effect of genes, codon positions, and time constraints. Evolution 59: 1653-1670.
    • (2005) Evolution , vol.59 , pp. 1653-1670
    • Magallón, S.A.1    Sanderson, M.J.2
  • 33
    • 33845617284 scopus 로고    scopus 로고
    • Freshwater paths across the ocean: Molecular phylogeny of the frog Ptychadena newtoni gives insights into amphibian colonization of oceanic islands
    • Measy, G.J., Vences, M., Drewes, R.C., Chiari, Y., Melo, M. & Boules, B. 2007. Freshwater paths across the ocean: Molecular phylogeny of the frog Ptychadena newtoni gives insights into amphibian colonization of oceanic islands. J. Biogeogr. 34: 7-20.
    • (2007) J. Biogeogr , vol.34 , pp. 7-20
    • Measy, G.J.1    Vences, M.2    Drewes, R.C.3    Chiari, Y.4    Melo, M.5    Boules, B.6
  • 35
    • 0000147290 scopus 로고
    • The implications of congruence in Menidia
    • Mickevich, M.F. & Farris, J.S. 1981. The implications of congruence in Menidia. Syst. Zool. 30: 351-370.
    • (1981) Syst. Zool , vol.30 , pp. 351-370
    • Mickevich, M.F.1    Farris, J.S.2
  • 37
    • 0028681223 scopus 로고
    • Parallel phylogenies: Reconstructing the history of host-parasite assemblages
    • Page, R.D.M. 1995a. Parallel phylogenies: Reconstructing the history of host-parasite assemblages. Cladistics 10: 155-173.
    • (1995) Cladistics , vol.10 , pp. 155-173
    • Page, R.D.M.1
  • 39
    • 0023822631 scopus 로고
    • Relationships between gene trees and species trees
    • Pamilo, P. & Nei, M. 1988. Relationships between gene trees and species trees. Molec. Biol. Evol. 5: 568-583.
    • (1988) Molec. Biol. Evol , vol.5 , pp. 568-583
    • Pamilo, P.1    Nei, M.2
  • 40
    • 31344454068 scopus 로고    scopus 로고
    • Tree disagreement: Measuring and testing incongruence in phylogenies
    • Planet, P.J. 2006. Tree disagreement: Measuring and testing incongruence in phylogenies. J. Biomed. Informatics 39: 86-102.
    • (2006) J. Biomed. Informatics , vol.39 , pp. 86-102
    • Planet, P.J.1
  • 41
    • 45849154165 scopus 로고    scopus 로고
    • ModelTest: Phylogenetic model averaging
    • Posada, D. 2008. ModelTest: Phylogenetic model averaging. Molec. Biol. Evol. 25: 1253-1256.
    • (2008) Molec. Biol. Evol , vol.25 , pp. 1253-1256
    • Posada, D.1
  • 42
    • 33845627286 scopus 로고    scopus 로고
    • The supermatrix approach to systematics
    • Queiroz, A. de & Gatesy, J. 2006. The supermatrix approach to systematics. Trends Ecol. Evol. 22: 34-41.
    • (2006) Trends Ecol. Evol , vol.22 , pp. 34-41
    • de Queiroz, A.1    Gatesy, J.2
  • 43
    • 0026822436 scopus 로고
    • Phylogenetic inference based on matrix representation of trees
    • Ragan, M.A. 1992. Phylogenetic inference based on matrix representation of trees. Molec. Phylog. Evol. 1: 53-58.
    • (1992) Molec. Phylog. Evol , vol.1 , pp. 53-58
    • Ragan, M.A.1
  • 44
    • 33745032085 scopus 로고    scopus 로고
    • Further problems with the incongruence length difference test: "hypercongruence" effect and multiple comparisons
    • Ramirez, M.J. 2006. Further problems with the incongruence length difference test: "hypercongruence" effect and multiple comparisons. Cladistics 22: 289-295.
    • (2006) Cladistics , vol.22 , pp. 289-295
    • Ramirez, M.J.1
  • 45
    • 0001466544 scopus 로고
    • A randomisation test of null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree
    • Rodrigo, A.G., Kelly-Borges, M., Bergquist, P.R. & Bergquist, L. 1993. A randomisation test of null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree. New Zealand J. Bot. 31: 257-268.
    • (1993) New Zealand J. Bot , vol.31 , pp. 257-268
    • Rodrigo, A.G.1    Kelly-Borges, M.2    Bergquist, P.R.3    Bergquist, L.4
  • 46
    • 0025267792 scopus 로고
    • The general stochastic model of nucleotide substitution
    • Rodriguez, F., Oliver, J.L., Marín, A. & Medina, J.R. 1990. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142: 485-501.
    • (1990) J. Theor. Biol , vol.142 , pp. 485-501
    • Rodriguez, F.1    Oliver, J.L.2    Marín, A.3    Medina, J.R.4
  • 47
    • 0033793019 scopus 로고    scopus 로고
    • Rare genomic changes as a tool for phylogenetics
    • Rokas, S. & Holland, P.M. 2000. Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 15: 454-459.
    • (2000) Trends Ecol. Evol , vol.15 , pp. 454-459
    • Rokas, S.1    Holland, P.M.2
  • 48
    • 0242365676 scopus 로고    scopus 로고
    • Genomescale approaches to resolving incongruence in molecular phylogenies
    • Rokas, A., Williams, B.L., King, N. & Carroll, S.B. 2003. Genomescale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798-804.
    • (2003) Nature , vol.425 , pp. 798-804
    • Rokas, A.1    Williams, B.L.2    King, N.3    Carroll, S.B.4
  • 49
    • 70349525316 scopus 로고    scopus 로고
    • Evolutionary relationships in the Spermacoceae alliance (Rubiaceae) using information from six molecular loci: Insights into systematic affinities of Neohymenopogon and Mouretia
    • Rydin, C., Razafimandimbison, S.G., Khodabandeh, A. & Bremer, B. 2009. Evolutionary relationships in the Spermacoceae alliance (Rubiaceae) using information from six molecular loci: Insights into systematic affinities of Neohymenopogon and Mouretia. Taxon 58: 793-810.
    • (2009) Taxon , vol.58 , pp. 793-810
    • Rydin, C.1    Razafimandimbison, S.G.2    Khodabandeh, A.3    Bremer, B.4
  • 50
    • 26444530167 scopus 로고    scopus 로고
    • Protein interactions limit the rate of evolution of photosynthetic genes in cyanobacteria
    • Shi, T., Bibby, T.S., Jiang, L., Irwin, A.J. & Falkowski, P.G. 2005. Protein interactions limit the rate of evolution of photosynthetic genes in cyanobacteria. Molec. Biol. Evol. 22: 2179-2189
    • (2005) Molec. Biol. Evol , vol.22 , pp. 2179-2189
    • Shi, T.1    Bibby, T.S.2    Jiang, L.3    Irwin, A.J.4    Falkowski, P.G.5
  • 51
    • 60849123934 scopus 로고    scopus 로고
    • Mega phylogeny approach for comparative biology: An alternative to supertree and supermatrix approaches
    • Doi:10.1186/1471-2148-9-37
    • Smith, S.A., Beaulieu, J.M. & Donoghue, M.J. 2009. Mega phylogeny approach for comparative biology: An alternative to supertree and supermatrix approaches. BMC Evol. Biol. 9: 37. Doi:10.1186/1471-2148-9-37.
    • (2009) BMC Evol. Biol , vol.9 , pp. 37
    • Smith, S.A.1    Beaulieu, J.M.2    Donoghue, M.J.3
  • 53
    • 38049165771 scopus 로고    scopus 로고
    • AxPoords & parallel AxParafit: Statistical co-phylogenetic analyses on thousands of taxa
    • Doi:10.1186/1471-2105-8-405
    • Stamatakis, A., Auch, A.F., Meier-Kolthoff, J. & Göker, M. 2007. AxPoords & parallel AxParafit: Statistical co-phylogenetic analyses on thousands of taxa. BMC Bioinformatics 8: 405. Doi:10.1186/1471-2105-8-405.
    • (2007) BMC Bioinformatics , vol.8 , pp. 405
    • Stamatakis, A.1    Auch, A.F.2    Meier-Kolthoff, J.3    Göker, M.4
  • 54
    • 0002671410 scopus 로고
    • Some probabilistic and statistical problems in the analysis of DNA sequences
    • Tawaré, S. 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. Lectures Math. Life Sci. 17: 57-86.
    • (1986) Lectures Math. Life Sci , vol.17 , pp. 57-86
    • Tawaré, S.1
  • 55
    • 0021084212 scopus 로고
    • Phylogenetic inference from restriction end onucleasecleavage site maps with particular reference to the humans and apes
    • Templeton, A.R. 1983. Phylogenetic inference from restriction end onucleasecleavage site maps with particular reference to the humans and apes. Evolution 37: 221-244.
    • (1983) Evolution , vol.37 , pp. 221-244
    • Templeton, A.R.1
  • 56
    • 0036803223 scopus 로고    scopus 로고
    • Divergence time and evolutionaryrate estimation with multilocus data
    • Thorne, J.L. & Kishino, H. 2002. Divergence time and evolutionaryrate estimation with multilocus data. Syst. Biol. 51: 689-702.
    • (2002) Syst. Biol , vol.51 , pp. 689-702
    • Thorne, J.L.1    Kishino, H.2
  • 57
    • 0002574561 scopus 로고    scopus 로고
    • Evolutionary trees of apes and humans from DNA sequences
    • in: Lock, A. & Peters, C.R. (eds.), Oxford: Clarendon Press
    • Wadell, P.J. & Penny, D. 1996. Evolutionary trees of apes and humans from DNA sequences. Pp. 53-73 in: Lock, A. & Peters, C.R. (eds.), Handbook of human symbolic evolution. Oxford: Clarendon Press.
    • (1996) Handbook of Human Symbolic Evolution , pp. 53-73
    • Wadell, P.J.1    Penny, D.2
  • 58
    • 0027132974 scopus 로고
    • Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
    • Yang, Z. 1993. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Molec. Biol. Evol. 10: 1396-1401.
    • (1993) Molec. Biol. Evol , vol.10 , pp. 1396-1401
    • Yang, Z.1
  • 59
    • 0028214103 scopus 로고
    • Estimating the pattern of nucleotide substitution
    • Yang, Z. 1994a. Estimating the pattern of nucleotide substitution. J. Molec. Evol. 39: 105-111.
    • (1994) J. Molec. Evol , vol.39 , pp. 105-111
    • Yang, Z.1
  • 60
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • Yang, Z. 1994b. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J. Molec. Evol. 39: 306-314.
    • (1994) J. Molec. Evol , vol.39 , pp. 306-314
    • Yang, Z.1
  • 61
    • 70349489103 scopus 로고    scopus 로고
    • Molecular phylogeny and biogeography of Gentiana sect. Cruciata (Gentianaceae) based on four chloroplast DNA datasets
    • Zhang, X.L., Wang, Y.J., Ge, X.J., Yuan, Y.M., Yang, H.L. & Liu, J.Q. 2009. Molecular phylogeny and biogeography of Gentiana sect. Cruciata (Gentianaceae) based on four chloroplast DNA datasets. Taxon 58: 862-870.
    • (2009) Taxon , vol.58 , pp. 862-870
    • Zhang, X.L.1    Wang, Y.J.2    Ge, X.J.3    Yuan, Y.M.4    Yang, H.L.5    Liu, J.Q.6


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