메뉴 건너뛰기




Volumn 8, Issue 6, 2011, Pages 1685-1691

From gene trees to species trees II: Species tree inference by minimizing deep coalescence events

Author keywords

deep coalescence; gene duplication and loss; Gene tree and species tree reconciliation; NP hardness; the parsimony principle

Indexed keywords

GENE DUPLICATIONS; GENE LOSS; GENE TREE; GENE TREE AND SPECIES TREE RECONCILIATION; HORIZONTAL GENE TRANSFER; LINEAR TIME; NP-HARD; NP-HARDNESS; PARSIMONY PRINCIPLE;

EID: 80052886059     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2011.83     Document Type: Article
Times cited : (56)

References (33)
  • 1
    • 46249107577 scopus 로고    scopus 로고
    • The Multiple Gene Duplication Problem Revisited
    • M.S. Bansal and O. Eulenstein, "The Multiple Gene Duplication Problem Revisited," Bioinformatics, vol. 24, pp. 132-138, 2008.
    • (2008) Bioinformatics , vol.24 , pp. 132-138
    • Bansal, M.S.1    Eulenstein, O.2
  • 2
    • 52449122374 scopus 로고    scopus 로고
    • Gene family evolution by duplication, speciation, and loss
    • C. Chauve, J.P. Doyon, and N. El-Mabrouk, "Gene Family Evolution by Duplication, Speciation, and Loss," J. Computational Biology, vol. 15, pp. 1043-1062, 2008.
    • (2008) J. Computational Biology , vol.15 , pp. 1043-1062
    • Chauve, C.1    Doyon, J.P.2    El-Mabrouk, N.3
  • 3
    • 0033692378 scopus 로고    scopus 로고
    • Notung: A program for dating gene duplications and optimizing gene family trees
    • K. Chen, D. Durand, and M. Farach-Colton, "Notung: A Program for Dating Gene Duplications and Optimizing Gene Family Trees," J. Computational Biology, vol. 7, pp. 429-447, 2000.
    • (2000) J. Computational Biology , vol.7 , pp. 429-447
    • Chen, K.1    Durand, D.2    Farach-Colton, M.3
  • 4
    • 13244292527 scopus 로고    scopus 로고
    • Gene tree distributions under the coalescent process
    • J.H. Degnan and L.A. Salter, "Gene Tree Distribution under the Coalescence Process," Evolution, vol. 59, pp. 24-37, 2005. (Pubitemid 40181296)
    • (2005) Evolution , vol.59 , Issue.1 , pp. 24-37
    • Degnan, J.H.1    Salter, L.A.2
  • 5
    • 0000989175 scopus 로고
    • Gene trees and species trees: Molecular systematics as one-character taxonomy
    • J.J. Doyle, "Gene Trees and Species Trees: Molecular Systematics as One-Character Taxonomy," Systematic Botany, vol. 17, pp. 144-163, 1992.
    • (1992) Systematic Botany , vol.17 , pp. 144-163
    • Doyle, J.J.1
  • 6
    • 33645981936 scopus 로고    scopus 로고
    • A hybrid micro-macro-evolutionary approach to gene tree reconstruction
    • D. Durand, B.V. Halldorsson, and B. Vernot, "A Hybrid Micro-Macro-evolutionary Approach to Gene Tree Reconstruction," J. Computational Biology, vol. 13, pp. 320-335, 2006.
    • (2006) J. Computational Biology , vol.13 , pp. 320-335
    • Durand, D.1    Halldorsson, B.V.2    Vernot, B.3
  • 7
    • 0034496840 scopus 로고    scopus 로고
    • Perspective: Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies
    • S.V. Edwards and P. Beerli, "Perspective: Gene Divergence, Population Divergence, and the Variance in Coalescence Time in Phylogeography Studies," Evolution, vol. 54, pp. 1839-1854, 2000. (Pubitemid 32113816)
    • (2000) Evolution , vol.54 , Issue.6 , pp. 1839-1854
    • Edwards, S.1    Beerli, P.2
  • 8
    • 0031949306 scopus 로고    scopus 로고
    • Duplication-based measures of difference between gene and species trees
    • O. Eulenstein, B. Mirkin, and M. Vingron, "Duplication-Based Measures of Difference between Gene and Species Trees," J. Computational Biology, vol. 5, pp. 135-148, 1998. (Pubitemid 28153011)
    • (1998) Journal of Computational Biology , vol.5 , Issue.1 , pp. 135-148
    • Eulenstein, O.1    Mirkin, B.2    Vingron, M.3
  • 9
    • 0014800108 scopus 로고
    • Distinguishing homologous from analogous proteins
    • W. Fitch, "Distinguishing Homologous from Analogous Proteins," Systematic Zoology, vol. 19, pp. 99-113, 1970.
    • (1970) Systematic Zoology , vol.19 , pp. 99-113
    • Fitch, W.1
  • 11
    • 0000365320 scopus 로고
    • Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences
    • M. Goodman, J. Czelusniak, G.W. Moore, A.E. Romero-Herrera, and G. Matsuda, "Fitting the Gene Lineage into Its Species Lineage, a Parsimony Strategy Illustrated by Cladograms Constructed from Globin Sequences," Systematic Zoology, vol. 28, pp. 132-163, 1979.
    • (1979) Systematic Zoology , vol.28 , pp. 132-163
    • Goodman, M.1    Czelusniak, J.2    Moore, G.W.3    Romero-Herrera, A.E.4    Matsuda, G.5
  • 12
    • 0030253222 scopus 로고    scopus 로고
    • Reconstruction of ancient molecular phylogeny
    • DOI 10.1006/mpev.1996.0071
    • R. Guigó, I. Muchnik, and T. Smith, "Reconstruction of Ancient Molecular Phylogeny," Molecular Phylogenetics and Evolution, vol. 6, pp. 189-213, 1996. (Pubitemid 126320615)
    • (1996) Molecular Phylogenetics and Evolution , vol.6 , Issue.2 , pp. 189-213
    • Guigo, R.1    Muchnik, I.2    Smith, T.F.3
  • 14
    • 3142714474 scopus 로고    scopus 로고
    • Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis
    • DOI 10.1534/genetics.103.024182
    • J. Hey and R. Nielsen, "Multilocus Methods for Estimating Population Sizes, Migration Rates and Divergence Time, with Applications to the Divergence of Drosophila pseudoobscura and D. persimilis," Genetics, vol. 167, pp. 747-760, 2004. (Pubitemid 38931862)
    • (2004) Genetics , vol.167 , Issue.2 , pp. 747-760
    • Hey, J.1    Nielsen, R.2
  • 15
    • 58149216660 scopus 로고    scopus 로고
    • On the computational complexity of the reticulate cophylogeny reconstruction problem
    • R. Libeskind-Hadas and M.A. Charleston, "On the Computational Complexity of the Reticulate Cophylogeny Reconstruction Problem," J. Computational Biology, vol. 16, pp. 105-117, 2009.
    • (2009) J. Computational Biology , vol.16 , pp. 105-117
    • Libeskind-Hadas, R.1    Charleston, M.A.2
  • 18
    • 0034938644 scopus 로고    scopus 로고
    • From gene trees to species trees
    • DOI 10.1137/S0097539798343362, PII S0097539798343362
    • B. Ma, M. Li, and L.X. Zhang, "From Gene Trees to Species Trees," SIAM J. Computing, vol. 30, pp. 729-752, 2001. (Pubitemid 32644732)
    • (2001) SIAM Journal on Computing , vol.30 , Issue.3 , pp. 729-752
    • Ma, B.1    Li, M.2    Zhang, L.3
  • 19
    • 0031504952 scopus 로고    scopus 로고
    • Gene trees in species trees
    • W.P. Maddison, "Gene Trees in Species Trees," Systematic Biology, vol. 46, pp. 523-536, 1997.
    • (1997) Systematic Biology , vol.46 , pp. 523-536
    • Maddison, W.P.1
  • 20
    • 33644606488 scopus 로고    scopus 로고
    • Inferring phylogeny despite incomplete lineage sorting
    • W.P. Maddison and L. Knowles, "Inferring Phylogeny despite Incomplete Lineage Sorting," Systematic Biology, vol. 55, pp. 21-30, 2006.
    • (2006) Systematic Biology , vol.55 , pp. 21-30
    • Maddison, W.P.1    Knowles, L.2
  • 21
    • 0029448349 scopus 로고
    • A biologically meaningful model for comparing molecular phylogenies
    • B. Mirkin, I. Muchnik, and T. Smith, "A Biologically Meaningful Model for Comparing Molecular Phylogenies," J. Computational Biology, vol. 2, pp. 493-507, 1995.
    • (1995) J. Computational Biology , vol.2 , pp. 493-507
    • Mirkin, B.1    Muchnik, I.2    Smith, T.3
  • 22
    • 11944269526 scopus 로고
    • Testing species phylogenies and phylogenetic methods with congruence
    • M.M. Miyamoto and W.T. Fitch, "Testing Species Phylogenies and Phylogenetic Methods with Congruence," Systematic Biology, vol. 44, pp. 64-76, 1995.
    • (1995) Systematic Biology , vol.44 , pp. 64-76
    • Miyamoto, M.M.1    Fitch, W.T.2
  • 24
    • 12044253257 scopus 로고
    • Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas
    • R. Page, "Maps between Trees and Cladistic Analysis of Historical Associations among Genes, Organisms, and Areas," Systematic Biology, vol. 43, pp. 58-77, 1994. (Pubitemid 24979624)
    • (1994) Systematic Biology , vol.43 , Issue.1 , pp. 58-77
    • Page, R.D.M.1
  • 25
    • 0031110886 scopus 로고    scopus 로고
    • From Gene to Organismal Phylogeny: Reconciled Trees and the Gene Tree/Species Tree Problem
    • DOI 10.1006/mpev.1996.0390, PII S1055790396903905
    • R. Page and M. Charleston, "From Gene to Organismal Phylogeny: Reconciled Trees and the Gene Tree/Species Tree Problem," Molecular Phylogenetics and Evolution, vol. 7, pp. 231-240, 1997. (Pubitemid 127345887)
    • (1997) Molecular Phylogenetics and Evolution , vol.7 , Issue.2 , pp. 231-240
    • Page, R.D.M.1    Charleston, M.A.2
  • 26
    • 0023822631 scopus 로고
    • Relationship between gene trees and species trees
    • P. Pamilo and M. Nei, "Relationship between Gene Trees and Species Trees," Molecular Biology Evolution, vol. 5, pp. 568-583, 1988.
    • (1988) Molecular Biology Evolution , vol.5 , pp. 568-583
    • Pamilo, P.1    Nei, M.2
  • 27
    • 0031430589 scopus 로고    scopus 로고
    • Phylogenetic approaches in coevolution and biogeography
    • PII S0300325698000087
    • F. Ronquist, "Phylogenetic Approaches in Coevolution and Biogeography," Zoologica Scripta, vol. 26, pp. 313-322, 1997. (Pubitemid 28224032)
    • (1997) Zoologica Scripta , vol.26 , Issue.4 , pp. 313-322
    • Ronquist, F.1
  • 28
    • 0036515730 scopus 로고    scopus 로고
    • The Probability of Topological Concordance of Gene Trees and Species Trees
    • DOI 10.1006/tpbi.2001.1568
    • N.A. Rosenberg, "The Probability of Topological Concordance of Gene Trees and Species Trees," Theoretical Population Biology, vol. 61, pp. 225-247, 2002. (Pubitemid 38042804)
    • (2002) Theoretical Population Biology , vol.61 , Issue.2 , pp. 225-247
    • Rosenberg, N.A.1
  • 30
    • 0024713112 scopus 로고
    • Gene genealogy in three related population: Consistency probability between gene and population trees
    • N. Takahata, "Gene Genealogy in Three Related Population: Consistency Probability between Gene and Population Trees," Genetics, vol. 122, pp. 957-966, 1989.
    • (1989) Genetics , vol.122 , pp. 957-966
    • Takahata, N.1
  • 31
    • 70349658769 scopus 로고    scopus 로고
    • Species tree inference by minimizing deep coalescences
    • doi:10.1371/journal.pcbi.1000501
    • C. Than and L. Nakhleh, "Species Tree Inference by Minimizing Deep Coalescences," PLoS Computational Biology, vol. 5, e1000501, 2009, doi:10.1371/journal.pcbi.1000501.
    • (2009) PLoS Computational Biology , vol.5
    • Than, C.1    Nakhleh, L.2
  • 32
    • 0026031181 scopus 로고
    • Inference of species phylogeny in relation to segregation of ancient polymorphisms
    • C.-I. Wu, "Inference of Species Phylogeny in Relation to Segregation of Ancient Polymorphisms," Genetics, vol. 127, pp. 429-435, 1991.
    • (1991) Genetics , vol.127 , pp. 429-435
    • Wu, C.-I.1
  • 33
    • 0030762443 scopus 로고    scopus 로고
    • On a mirkin-muchnik-smith conjecture for comparing molecular phylogenies
    • L.X. Zhang, "On a Mirkin-Muchnik-Smith Conjecture for Comparing Molecular Phylogenies," J. Computational Biology, vol. 4, pp. 177-188, 1997.
    • (1997) J. Computational Biology , vol.4 , pp. 177-188
    • Zhang, L.X.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.