메뉴 건너뛰기




Volumn 10, Issue 1, 2011, Pages

Performance of Matrix representation with parsimony for inferring species from gene trees

Author keywords

consensus; phylogenetics; phylogenomics; rooted triple; statistical consistency; supertree

Indexed keywords

ARTICLE; CELL LINEAGE; CELL SELECTION; MATRIX REPRESENTATION WITH PARSIMONY; PARSIMONY ANALYSIS; PERFORMANCE; PHYLOGENOMICS; SPECIES IDENTIFICATION; TAXON; TREE;

EID: 79958164317     PISSN: None     EISSN: 15446115     Source Type: Journal    
DOI: 10.2202/1544-6115.1611     Document Type: Article
Times cited : (18)

References (54)
  • 1
    • 79956154434 scopus 로고    scopus 로고
    • Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent
    • in press, DOI:10.1007/s00285-010-0355-7
    • Allman, E. S., J. H. Degnan, and J. A. Rhodes (2011): "Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent", J. Math. Biol., in press, DOI:10.1007/s00285-010-0355-7.
    • (2011) J. Math. Biol.
    • Allman, E.S.1    Degnan, J.H.2    Rhodes, J.A.3
  • 3
    • 0002844544 scopus 로고
    • Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees
    • Baum, B. R. (1992): "Combining trees as a way of combining data sets 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
  • 4
    • 0032148631 scopus 로고    scopus 로고
    • Properties of Matrix Representation with Parsimony Analyses
    • Bininda-Emonds, O. R. P. and H. N. Bryant (1998): "Properties of matrix representation with parsimony analyses", Syst. Biol., 47, 497-508. (Pubitemid 128451088)
    • (1998) Systematic Biology , vol.47 , Issue.3 , pp. 497-508
    • Bininda-Emonds, O.R.P.1    Bryant, H.N.2
  • 5
    • 0035527411 scopus 로고    scopus 로고
    • Assessment of the accuracy of matrix representation with parsimony analysis supertree construction
    • Bininda-Emonds, O. R. P. and M. J. Sanderson (2001): "Assessment of the accuracy of matrix representation with parsimony analysis supertree construction", Syst. Biol., 50, 565-579.
    • (2001) Syst. Biol. , vol.50 , pp. 565-579
    • Bininda-Emonds, O.R.P.1    Sanderson, M.J.2
  • 6
    • 1642519173 scopus 로고    scopus 로고
    • A classification of consensus methods for phylogenies
    • M. Janowitz, F. J. Lapointe, F. R. McMorris, B. Mirkin, and F. S. Roberts, eds., DIMACS. AMS.
    • Bryant, D. (2003): "A classification of consensus methods for phylogenies", in M. Janowitz, F. J. Lapointe, F. R. McMorris, B. Mirkin, and F. S. Roberts, eds., BioConsensus, DIMACS. AMS., 163-183.
    • (2003) BioConsensus , pp. 163-183
    • Bryant, D.1
  • 7
    • 67149088756 scopus 로고    scopus 로고
    • The size of a maximum agreement subtree for random binary trees
    • M. Janowitz, F. J. Lapointe, F. R. McMorris, B. Mirkin, and F. S. Roberts, eds., DIMACS. AMS.
    • Bryant, D., A. McKenzie, and M. Steel (2003): "The size of a maximum agreement subtree for random binary trees", in M. Janowitz, F. J. Lapointe, F. R. McMorris, B. Mirkin, and F. S. Roberts, eds., BioConsensus, DIMACS. AMS., 55-65.
    • (2003) BioConsensus , pp. 55-65
    • Bryant, D.1    McKenzie, A.2    Steel, M.3
  • 8
    • 40849120246 scopus 로고    scopus 로고
    • Integrating phylogenetic and population genetic analyses of multiple loci to test species divergence hypotheses in Passerina buntings
    • DOI 10.1534/genetics.107.076422
    • Carling, M. and R. Brumfield (2008): "Integrating phylogenetic and population genetic analyses of multiple loci to test species divergence hypotheses in Passerina buntings", Genetics, 178, 363-377. (Pubitemid 351398753)
    • (2008) Genetics , vol.178 , Issue.1 , pp. 363-377
    • Carling, M.D.1    Brumfield, R.T.2
  • 9
    • 57649143466 scopus 로고    scopus 로고
    • Supertrees join the mainstream of phylogenetics
    • Cotton, J. A. and M. Wilkinson (2009): "Supertrees join the mainstream of phylogenetics", Trends Ecol. Evol., 24, 1-3.
    • (2009) Trends Ecol. Evol. , vol.24 , pp. 1-3
    • Cotton, J.A.1    Wilkinson, M.2
  • 10
    • 13844250623 scopus 로고    scopus 로고
    • Clann: Investigating phylogenetic information through supertree analyses
    • DOI 10.1093/bioinformatics/bti020
    • Creevey, C. J. and J. O. McInerney (2005): "Clann: investigating phylogenetic information through supertree analyses", Bioinformatics, 21, 390-392. (Pubitemid 40246612)
    • (2005) Bioinformatics , vol.21 , Issue.3 , pp. 390-392
    • Creevey, C.J.1    McInerney, J.O.2
  • 11
    • 79958154067 scopus 로고    scopus 로고
    • Probabilities of gene trees with intraspecific sampling given a species tree
    • L. L. Knowles and L. S. Kubatko, eds., Hoboken, NJ: Wiley-Blackwell
    • Degnan, J. H. (2010): "Probabilities of gene trees with intraspecific sampling given a species tree", in L. L. Knowles and L. S. Kubatko, eds., Estimating Species Trees: Practical and Theoretical Aspects, Hoboken, NJ: Wiley-Blackwell, 53-78.
    • (2010) Estimating Species Trees: Practical and Theoretical Aspects , pp. 53-78
    • Degnan, J.H.1
  • 12
    • 67449167484 scopus 로고    scopus 로고
    • Properties of consensus methods for estimating species trees from gene trees
    • Degnan, J. H., M. DeGiorgio, D. Bryant, and N. A. Rosenberg (2009): "Properties of consensus methods for estimating species trees from gene trees", Syst. Biol., 58, 35-54.
    • (2009) Syst. Biol. , vol.58 , pp. 35-54
    • Degnan, J.H.1    DeGiorgio, M.2    Bryant, D.3    Rosenberg, N.A.4
  • 13
    • 33646928341 scopus 로고    scopus 로고
    • Discordance of species trees with their most likely gene trees
    • DOI 10.1371/journal.pgen.0020068
    • Degnan, J. H. and N. A. Rosenberg (2006): "Discordance of species trees with their most likely gene trees", PLoS Genetics, 2, 762-768. (Pubitemid 43794324)
    • (2006) PLoS Genetics , vol.2 , Issue.5 , pp. 762-768
    • Degnan, J.H.1    Rosenberg, N.A.2
  • 14
    • 65649131928 scopus 로고    scopus 로고
    • Gene tree discordance, phylogenetic inference and the multispecies coalescent
    • Degnan, J. H. and N. A. Rosenberg (2009): "Gene tree discordance, phylogenetic inference and the multispecies coalescent", Trends Ecol. Evol, 24, 332-340.
    • (2009) Trends Ecol. Evol. , vol.24 , pp. 332-340
    • Degnan, J.H.1    Rosenberg, N.A.2
  • 15
    • 13244292527 scopus 로고    scopus 로고
    • Gene tree distributions under the coalescent process
    • Degnan, J. H. and L. A. Salter (2005): "Gene tree distributions under the coalescent process", Evolution, 59, 24-37. (Pubitemid 40181296)
    • (2005) Evolution , vol.59 , Issue.1 , pp. 24-37
    • Degnan, J.H.1    Salter, L.A.2
  • 16
    • 38849124790 scopus 로고    scopus 로고
    • Coalescent time distributions in trees of arbitrary size
    • Article 2
    • Efromovich, S. and L. S. Kubatko (2008): "Coalescent time distributions in trees of arbitrary size", Stat. App. in Genet. Mol. Biol., 7, Article 2.
    • (2008) Stat. App. in Genet. Mol. Biol. , vol.7
    • Efromovich, S.1    Kubatko, L.S.2
  • 18
    • 38449096427 scopus 로고    scopus 로고
    • A model of horizontal gene transfer and the bacterial phylogeny problem
    • Galtier, N. (2007): "A model of horizontal gene transfer and the bacterial phylogeny problem", Syst. Biol., 56, 633-642.
    • (2007) Syst. Biol. , vol.56 , pp. 633-642
    • Galtier, N.1
  • 19
    • 34447286481 scopus 로고    scopus 로고
    • How many genes should a systematist sample? Conflicting insights from a phylogenomic matrix characterized by replicated incongruence
    • Gatesy, J., R. DeSalle, and N. Wahlberg (2007): "How many genes should a systematist sample? Conflicting insights from a phylogenomic matrix characterized by replicated incongruence", Syst. Biol., 56, 355-363.
    • (2007) Syst. Biol. , vol.56 , pp. 355-363
    • Gatesy, J.1    DeSalle, R.2    Wahlberg, N.3
  • 20
    • 70450237691 scopus 로고    scopus 로고
    • What is the danger of the anomaly zone for empirical phylogenetics?
    • Huang, H. and L. L. Knowles (2009): "What is the danger of the anomaly zone for empirical phylogenetics?" Syst. Biol., 58, 527-536.
    • (2009) Syst. Biol. , vol.58 , pp. 527-536
    • Huang, H.1    Knowles, L.L.2
  • 21
    • 25644452054 scopus 로고    scopus 로고
    • Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees
    • Jennings, W. B. and S. V. Edwards (2005): "Speciational history of Australian grassfinches (Poephila) inferred from thirty gene trees", Evolution, 59, 2033-2047. (Pubitemid 41384386)
    • (2005) Evolution , vol.59 , Issue.9 , pp. 2033-2047
    • Jennings, W.B.1    Edwards, S.V.2
  • 22
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • H. N. Munro, ed., Academic Press, NY
    • Jukes, T. H. and C. R. Cantor (1969): "Evolution of protein molecules", in H. N. Munro, ed., Mammalian Protein Metabolism, Academic Press, NY, 21-132.
    • (1969) Mammalian Protein Metabolism , pp. 21-132
    • Jukes, T.H.1    Cantor, C.R.2
  • 23
    • 63549118031 scopus 로고    scopus 로고
    • STEM: Species tree estimation using maximum likelihood for gene trees under coalescence
    • Kubatko, L. S., B. C. Carstens, and L. L. Knowles (2009): "STEM: species tree estimation using maximum likelihood for gene trees under coalescence", Bioinformatics, 25, 971-973.
    • (2009) Bioinformatics , vol.25 , pp. 971-973
    • Kubatko, L.S.1    Carstens, B.C.2    Knowles, L.L.3
  • 24
    • 33847302458 scopus 로고    scopus 로고
    • Inconsistency of phylogenetic estimates from concatenated data under coalescence
    • Kubatko, L. S. and J. H. Degnan (2007): "Inconsistency of phylogenetic estimates from concatenated data under coalescence", Syst. Biol., 56, 17-24.
    • (2007) Syst. Biol. , vol.56 , pp. 17-24
    • Kubatko, L.S.1    Degnan, J.H.2
  • 25
    • 78649687580 scopus 로고    scopus 로고
    • Accuracy of phylogeny reconstruction methods combining overlapping gene data sets
    • Kupczok, A., H. A. Schmidt, and A. von Haeseler (2010): "Accuracy of phylogeny reconstruction methods combining overlapping gene data sets", Algorithms Mol. Biol., 5, 37.
    • (2010) Algorithms Mol. Biol. , vol.5 , pp. 37
    • Kupczok, A.1    Schmidt, H.A.2    Von Haeseler, A.3
  • 26
    • 78149256307 scopus 로고    scopus 로고
    • BUCKy: Gene tree/species tree reconciliation with Bayesian Concordance Analysis
    • Larget, B., S. K. Kotha, C. N. Dewey, and C. Ané (2010): "BUCKy: gene tree/species tree reconciliation with Bayesian Concordance Analysis", Bioinformatics, 26, 2910-2911.
    • (2010) Bioinformatics , vol.26 , pp. 2910-2911
    • Larget, B.1    Kotha, S.K.2    Dewey, C.N.3    Ané, C.4
  • 27
    • 77952468997 scopus 로고    scopus 로고
    • Total evidence, average consensus and matrix representation with parsimony: What a difference distances make
    • Levasseur, C. and F.-J. Lapointe (2006): "Total evidence, average consensus and matrix representation with parsimony: What a difference distances make", Evol. Bioinform., 2, 1-5.
    • (2006) Evol. Bioinform. , vol.2 , pp. 1-5
    • Levasseur, C.1    Lapointe, F.-J.2
  • 28
    • 77957686501 scopus 로고    scopus 로고
    • A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
    • Liu, L., L. Yu, and S. V. Edwards (2010a): "A maximum pseudo-likelihood approach for estimating species trees under the coalescent model", BMC Evol. Biol., 10, 302.
    • (2010) BMC Evol. Biol. , vol.10 , pp. 302
    • Liu, L.1    Yu, L.2    Edwards, S.V.3
  • 29
    • 70350247510 scopus 로고    scopus 로고
    • Maximum tree: A consistent estimator of the species tree
    • Liu, L., L. Yu, and D. K. Pearl (2010b): "Maximum tree: a consistent estimator of the species tree", J. Math. Biol., 60, 95-106.
    • (2010) J. Math. Biol. , vol.60 , pp. 95-106
    • Liu, L.1    Yu, L.2    Pearl, D.K.3
  • 30
    • 70349425459 scopus 로고    scopus 로고
    • Estimating species phylogenies using coalescence times among sequences
    • Liu, L., L. Yu, D. K. Pearl, and S. V. Edwards (2009): "Estimating species phylogenies using coalescence times among sequences", Syst. Biol., 58, 468-477.
    • (2009) Syst. Biol. , vol.58 , pp. 468-477
    • Liu, L.1    Yu, L.2    Pearl, D.K.3    Edwards, S.V.4
  • 31
    • 0031504952 scopus 로고    scopus 로고
    • Gene trees in species trees
    • Maddison, W. P. (1997): "Gene trees in species trees", Syst. Biol., 46, 523-536.
    • (1997) Syst. Biol. , vol.46 , pp. 523-536
    • Maddison, W.P.1
  • 32
    • 33644606488 scopus 로고    scopus 로고
    • Inferring phylogeny despite incomplete lineage sorting
    • Maddison, W. P. and L. L. Knowles (2006): "Inferring phylogeny despite incomplete lineage sorting", Syst. Biol., 55, 21-30.
    • (2006) Syst. Biol. , vol.55 , pp. 21-30
    • Maddison, W.P.1    Knowles, L.L.2
  • 33
    • 76849102326 scopus 로고    scopus 로고
    • Incomplete lineage sorting: Consistent phylogeny estimation from multiple loci
    • Mossel, E. and S. Roch (2010): "Incomplete lineage sorting: consistent phylogeny estimation from multiple loci", IEEE Comp. Bio. Bioinformatics, 7, 166-171.
    • (2010) IEEE Comp. Bio. Bioinformatics , vol.7 , pp. 166-171
    • Mossel, E.1    Roch, S.2
  • 35
    • 1042304216 scopus 로고    scopus 로고
    • APE: Analyses of phylogenetics and evolution in R language
    • DOI 10.1093/bioinformatics/btg412
    • Paradis, E., J. Claude, and K. Strimmer (2004): "APE: analyses of phylogenetics and evolution in R language", Bioinformatics, 20, 289-290. (Pubitemid 38195693)
    • (2004) Bioinformatics , vol.20 , Issue.2 , pp. 289-290
    • Paradis, E.1    Claude, J.2    Strimmer, K.3
  • 36
    • 0026822436 scopus 로고
    • Phylogenetic inference based on matrix representation of trees
    • Ragan, M. A. (1992): "Phylogenetic inference based on matrix representation of trees", Mol. Phylogenet. Evol., 1, 53-58.
    • (1992) Mol. Phylogenet. Evol. , vol.1 , pp. 53-58
    • Ragan, M.A.1
  • 37
    • 0030928378 scopus 로고    scopus 로고
    • Seq-gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • Rambaut, A. and N. C. Grassly (1997): "Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along evolutionary trees", Comput. Appl. Biosci., 13, 235-238. (Pubitemid 27249927)
    • (1997) Computer Applications in the Biosciences , vol.13 , Issue.3 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 38
    • 0041817551 scopus 로고    scopus 로고
    • Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci
    • Rannala, B. and Z. Yang (2003): "Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci", Genetics, 164, 1645-1656. (Pubitemid 37102224)
    • (2003) Genetics , vol.164 , Issue.4 , pp. 1645-1656
    • Rannala, B.1    Yang, Z.2
  • 39
    • 52949152371 scopus 로고    scopus 로고
    • Phlogenetic inference using whole genomes
    • Rannala, B. and Z. Yang (2008): "Phlogenetic inference using whole genomes", Annu. Rev. Genom. Human Genet., 9, 217-231.
    • (2008) Annu. Rev. Genom. Human Genet. , vol.9 , pp. 217-231
    • Rannala, B.1    Yang, Z.2
  • 40
    • 77954209722 scopus 로고    scopus 로고
    • SUPERTRIPLETS: A triplet-based supertree approach to phylogenomics
    • iSMB 2010
    • Ranwez, V., A. Criscuolo, and E. J. P. Douzery (2010): "SUPERTRIPLETS: a triplet-based supertree approach to phylogenomics", Bioinformatics, 26 iSMB 2010, i115-i123.
    • (2010) Bioinformatics , vol.26
    • Ranwez, V.1    Criscuolo, A.2    Douzery, E.J.P.3
  • 41
    • 0242365676 scopus 로고    scopus 로고
    • Genome-scale approaches to resolving incongruence in molecular phylogenies
    • DOI 10.1038/nature02053
    • Rokas, A., B. Williams, N. King, and S. Carroll (2003): "Genome-scale approaches to resolving incongruence in molecular phylogenies", Nature, 425, 798-804. (Pubitemid 37355944)
    • (2003) Nature , vol.425 , Issue.6960 , pp. 798-804
    • Rokas, A.1    Williams, B.I.2    King, N.3    Carroll, S.B.4
  • 42
    • 0036515730 scopus 로고    scopus 로고
    • The Probability of Topological Concordance of Gene Trees and Species Trees
    • DOI 10.1006/tpbi.2001.1568
    • Rosenberg, N. A. (2002): "The probability of topological concordance of gene trees and species trees", Theor. Popul. Biol., 61, 225-247. (Pubitemid 38042804)
    • (2002) Theoretical Population Biology , vol.61 , Issue.2 , pp. 225-247
    • Rosenberg, N.A.1
  • 43
    • 34248368417 scopus 로고    scopus 로고
    • Counting coalescent histories
    • DOI 10.1089/cmb.2006.0109
    • Rosenberg, N. A. (2007): "Counting coalescent histories", J. Comp. Biol., 14, 360-377. (Pubitemid 46742190)
    • (2007) Journal of Computational Biology , vol.14 , Issue.3 , pp. 360-377
    • Rosenberg, N.A.1
  • 44
    • 47749087905 scopus 로고    scopus 로고
    • Discordance of species trees with their most likely gene trees: The case of five taxa
    • Rosenberg, N. A. and R. Tao (2008): "Discordance of species trees with their most likely gene trees: the case of five taxa", Syst. Biol., 57, 131-140.
    • (2008) Syst. Biol. , vol.57 , pp. 131-140
    • Rosenberg, N.A.1    Tao, R.2
  • 45
    • 77952490857 scopus 로고    scopus 로고
    • Phylogenomics with incomplete taxon coverage: The limits to inference
    • Sanderson, M. J., M. M. McMahon, and M. Steel (2010): "Phylogenomics with incomplete taxon coverage: the limits to inference", BMC Evolut. Biol., 10, 155.
    • (2010) BMC Evolut. Biol. , vol.10 , pp. 155
    • Sanderson, M.J.1    McMahon, M.M.2    Steel, M.3
  • 46
    • 0042601470 scopus 로고    scopus 로고
    • Oxford, UK: Oxford University Press
    • Semple, C. and M. Steel (2003): Phylogenetics, Oxford, UK: Oxford University Press.
    • (2003) Phylogenetics
    • Semple, C.1    Steel, M.2
  • 47
    • 0031296691 scopus 로고    scopus 로고
    • Inferring Species Trees from Gene Trees: A Phylogenetic Analysis of the Elapidae (Serpentes) Based on the Amino Acid Sequences of Venom Proteins
    • DOI 10.1006/mpev.1997.0434, PII S1055790397904346
    • Slowinski, J. B., A. Knight, and A. P. Rooney (1997): "Inferring species trees from gene trees: A phylogenetic analysis of the Elapidae (Serpentes) based on the amino acid sequences of venom proteins", Mol. Phylogenet. Evol., 8, 349-362. (Pubitemid 127347894)
    • (1997) Molecular Phylogenetics and Evolution , vol.8 , Issue.3 , pp. 349-362
    • Slowinski, J.B.1    Knight, A.2    Rooney, A.P.3
  • 48
    • 41849131023 scopus 로고    scopus 로고
    • Maximum likelihood supertrees
    • DOI 10.1080/10635150802033014, PII 792022181
    • Steel, M. and A. Rodrigo (2008): "Maximum likelihood supertrees", Syst. Biol., 57, 243-250. (Pubitemid 351502944)
    • (2008) Systematic Biology , vol.57 , Issue.2 , pp. 243-250
    • Steel, M.1    Rodrigo, A.2
  • 50
    • 70349658769 scopus 로고    scopus 로고
    • Species tree inference by minimizing deep coalescences
    • Than, C. and L. Nakhleh (2009): "Species tree inference by minimizing deep coalescences", PLoS Comput. Biol., 5, e1000501.
    • (2009) PLoS Comput. Biol. , vol.5
    • Than, C.1    Nakhleh, L.2
  • 51
    • 78651298101 scopus 로고    scopus 로고
    • Consistency properties of species tree inference by minimizing deep coalescences
    • Than, C. V. and N. A. Rosenberg (2011): "Consistency properties of species tree inference by minimizing deep coalescences", J. Comput. Biol., 18, 1-15.
    • (2011) J. Comput. Biol. , vol.18 , pp. 1-15
    • Than, C.V.1    Rosenberg, N.A.2
  • 52
    • 65649112683 scopus 로고    scopus 로고
    • Greenwood Village, CO: Roberts & Company
    • Wakeley, J. (2008): Coalescent Theory, Greenwood Village, CO: Roberts & Company.
    • (2008) Coalescent Theory
    • Wakeley, J.1
  • 54
    • 59649117844 scopus 로고    scopus 로고
    • Robustness of topological supertree methods for reconciling dense incompatible data
    • Willson, S. J. (2009): "Robustness of topological supertree methods for reconciling dense incompatible data", IEEE-ACM Trans. Comput. Biol. Bioinf., 6, 62-75.
    • (2009) IEEE-ACM Trans. Comput. Biol. Bioinf. , vol.6 , pp. 62-75
    • Willson, S.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.