메뉴 건너뛰기




Volumn 7875 LNBI, Issue , 2013, Pages 261-272

Effect of incomplete lineage sorting on tree-reconciliation-based inference of gene duplication

Author keywords

[No Author keywords available]

Indexed keywords

DUPLICATION EVENTS; GENE DUPLICATIONS; GENE FAMILIES; GENE TREE; RANDOM GENES; STOCHASTIC VARIATION; TOPOLOGICAL PARAMETERS;

EID: 84883348775     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-38036-5_26     Document Type: Conference Paper
Times cited : (2)

References (38)
  • 2
    • 84863524200 scopus 로고    scopus 로고
    • Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss
    • Bansal, M.S., Alm, E.J., Kellis, M.: Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss. Bioinformatics 28(12), i283-i291 (2012)
    • (2012) Bioinformatics , vol.28 , Issue.12
    • Bansal, M.S.1    Alm, E.J.2    Kellis, M.3
  • 3
    • 33746433923 scopus 로고    scopus 로고
    • Optimal gene trees from sequences and species trees using a soft interpretation of parsimony
    • Berglund-Sonnhammer, A.C., Steffansson, P., Betts, M.J., Liberles, D.A.: Optimal gene trees from sequences and species trees using a soft interpretation of parsimony. J. Mol. Evol. 63(2), 240-250 (2006)
    • (2006) J. Mol. Evol. , vol.63 , Issue.2 , pp. 240-250
    • Berglund-Sonnhammer, A.C.1    Steffansson, P.2    Betts, M.J.3    Liberles, D.A.4
  • 4
    • 0023163377 scopus 로고
    • Mitochondrial DNA and human evolution
    • Cann, R.L., Stoneking, M., Wilson, A.C.: Mitochondrial DNA and human evolution. Nature 325(6099), 31-36 (1987)
    • (1987) Nature , vol.325 , Issue.6099 , pp. 31-36
    • Cann, R.L.1    Stoneking, M.2    Wilson, A.C.3
  • 5
    • 67650324396 scopus 로고    scopus 로고
    • New perspectives on gene family evolution: Losses in reconciliation and a link with supertrees
    • Batzoglou, S. (ed.) RECOMB 2009. Springer, Heidelberg
    • Chauve, C., El-Mabrouk, N.: New perspectives on gene family evolution: Losses in reconciliation and a link with supertrees. In: Batzoglou, S. (ed.) RECOMB 2009. LNCS, vol. 5541, pp. 46-58. Springer, Heidelberg (2009)
    • (2009) LNCS , vol.5541 , pp. 46-58
    • Chauve, C.1    El-Mabrouk, N.2
  • 6
    • 0033692378 scopus 로고    scopus 로고
    • Notung: A program for dating gene duplications and optimizing gene family trees
    • Chen, K., Durand, D., Farach-Colton, M.: Notung: a program for dating gene duplications and optimizing gene family trees. J. Comput. Biol. 7(3-4), 429-447 (2000)
    • (2000) J. Comput. Biol. , vol.7 , Issue.3-4 , pp. 429-447
    • Chen, K.1    Durand, D.2    Farach-Colton, M.3
  • 7
    • 13244292527 scopus 로고    scopus 로고
    • Gene tree distributions under the coalescent process
    • Degnan, J.H., Salter, L.A.: Gene tree distributions under the coalescent process. Evolution 59(1), 24-37 (2005)
    • (2005) Evolution , vol.59 , Issue.1 , pp. 24-37
    • Degnan, J.H.1    Salter, L.A.2
  • 8
    • 0000989175 scopus 로고
    • Gene trees and species trees: Molecular systematics as one-character taxonomy
    • Doyle, J.J.: Gene trees and species trees: molecular systematics as one-character taxonomy. Syst. Botany 17, 144-163 (1992)
    • (1992) Syst. Botany , vol.17 , pp. 144-163
    • Doyle, J.J.1
  • 9
    • 78649930876 scopus 로고    scopus 로고
    • An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers
    • Tannier, E. (ed.) RECOMB-CG 2010. Springer, Heidelberg
    • Doyon, J.-P., Scornavacca, C., Gorbunov, K.Y., Szöllo{combining double acute accent}si, G.J., Ranwez, V., Berry, V.: An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers. In: Tannier, E. (ed.) RECOMB-CG 2010. LNCS, vol. 6398, pp. 93-108. Springer, Heidelberg (2010)
    • (2010) LNCS , vol.6398 , pp. 93-108
    • Doyon, J.-P.1    Scornavacca, C.2    Gorbunov, K.Y.3    Szöllosi, G.J.4    Ranwez, V.5    Berry, V.6
  • 10
    • 58249100073 scopus 로고    scopus 로고
    • Is a new and general theory of molecular systematics emerging?
    • Edwards, S.V.: Is a new and general theory of molecular systematics emerging? Evolution 63(1), 1-19 (2008)
    • (2008) Evolution , vol.63 , Issue.1 , pp. 1-19
    • Edwards, S.V.1
  • 11
    • 0034496840 scopus 로고    scopus 로고
    • Perspective: Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies
    • Edwards, S.V., Beerli, P.: Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54(6), 1839-1854 (2000)
    • (2000) Evolution , vol.54 , Issue.6 , pp. 1839-1854
    • Edwards, S.V.1    Beerli, P.2
  • 12
    • 0000365320 scopus 로고
    • Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences
    • Goodman, M., Czelusniak, J., Moore, G.W., Romero-Herrera, A.E., Matsuda, G.: Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Biol. 28(2), 132-163 (1979)
    • (1979) Syst. Biol. , vol.28 , Issue.2 , pp. 132-163
    • Goodman, M.1    Czelusniak, J.2    Moore, G.W.3    Romero-Herrera, A.E.4    Matsuda, G.5
  • 13
    • 33746345337 scopus 로고    scopus 로고
    • DLS-trees: A model of evolutionary scenarios
    • Górecki, P., Tiuryn, J.: DLS-trees: a model of evolutionary scenarios. Theor. Comput. Sci. 359(1), 378-399 (2006)
    • (2006) Theor. Comput. Sci. , vol.359 , Issue.1 , pp. 378-399
    • Górecki, P.1    Tiuryn, J.2
  • 14
    • 37249034790 scopus 로고    scopus 로고
    • Bias in phylogenetic tree reconciliation methods: Implications for vertebrate genome evolution
    • Hahn, M.W.: Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution. Genome Biol. 8(7), R141 (2007)
    • (2007) Genome Biol. , vol.8 , Issue.7
    • Hahn, M.W.1
  • 15
    • 36048950933 scopus 로고    scopus 로고
    • Gene family evolution across 12 Drosophila genomes
    • Hahn, M.W., Han, M.V., Han, S.G.: Gene family evolution across 12 Drosophila genomes. PLoS Genetics 3(11), e197 (2007)
    • (2007) PLoS Genetics , vol.3 , Issue.11
    • Hahn, M.W.1    Han, M.V.2    Han, S.G.3
  • 16
    • 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
    • Hey, J., Nielsen, R.: Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167(2), 747-760 (2004)
    • (2004) Genetics , vol.167 , Issue.2 , pp. 747-760
    • Hey, J.1    Nielsen, R.2
  • 17
    • 47649104484 scopus 로고    scopus 로고
    • Horizontal gene transfer in eukaryotic evolution
    • Keeling, P.J., Palmer, J.D.: Horizontal gene transfer in eukaryotic evolution. Nat. Rev. Genet. 9(8), 605-618 (2008)
    • (2008) Nat. Rev. Genet. , vol.9 , Issue.8 , pp. 605-618
    • Keeling, P.J.1    Palmer, J.D.2
  • 20
    • 0034938644 scopus 로고    scopus 로고
    • From gene trees to species trees
    • Ma, B., Li, M., Zhang, L.X.: From gene trees to species trees. SIAM J. Comput. 30(3), 729-752 (2000)
    • (2000) SIAM J. Comput. , vol.30 , Issue.3 , pp. 729-752
    • Ma, B.1    Li, M.2    Zhang, L.X.3
  • 21
    • 0031504952 scopus 로고    scopus 로고
    • Gene trees in species trees
    • Maddison, W.P.: Gene trees in species trees. Syst. Biol. 46(3), 523-536 (1997)
    • (1997) Syst. Biol. , vol.46 , Issue.3 , pp. 523-536
    • Maddison, W.P.1
  • 22
    • 33644606488 scopus 로고    scopus 로고
    • Inferring phylogeny despite incomplete lineage sorting
    • Maddison, W.P., Knowles, L.L.: Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55(1), 21-30 (2006)
    • (2006) Syst. Biol. , vol.55 , Issue.1 , pp. 21-30
    • Maddison, W.P.1    Knowles, L.L.2
  • 23
    • 12044253257 scopus 로고
    • Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas
    • Page, R.D.M.: Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Syst. Biol. 43(1), 58-77 (1994)
    • (1994) Syst. Biol. , vol.43 , Issue.1 , pp. 58-77
    • Page, R.D.M.1
  • 24
    • 0023822631 scopus 로고
    • Relationships between gene trees and species trees
    • Pamilo, P., Nei, M.: Relationships between gene trees and species trees. Mol. Biol. Evol. 5(5), 568-583 (1988)
    • (1988) Mol. Biol. Evol. , vol.5 , Issue.5 , pp. 568-583
    • Pamilo, P.1    Nei, M.2
  • 25
    • 33750437728 scopus 로고    scopus 로고
    • Widespread discordance of gene trees with species tree in Drosophila: Evidence for incomplete lineage sorting
    • Pollard, D.A., Iyer, V.N., Moses, A.M., Eisen, M.B.: Widespread discordance of gene trees with species tree in Drosophila : evidence for incomplete lineage sorting. PLoS Genet. 2(10), e173 (2006)
    • (2006) PLoS Genet. , vol.2 , Issue.10
    • Pollard, D.A.1    Iyer, V.N.2    Moses, A.M.3    Eisen, M.B.4
  • 26
    • 84859546516 scopus 로고    scopus 로고
    • Unified modeling of gene duplication, loss, and coalescence using a locus tree
    • Rasmussen, M.D., Kellis, M.: Unified modeling of gene duplication, loss, and coalescence using a locus tree. Genome Research 22(4), 755-765 (2012)
    • (2012) Genome Research , vol.22 , Issue.4 , pp. 755-765
    • Rasmussen, M.D.1    Kellis, M.2
  • 27
    • 0036515730 scopus 로고    scopus 로고
    • The probability of topological concordance of gene trees and species trees
    • Rosenberg, N.A.: The probability of topological concordance of gene trees and species trees. Theor. Popul. Biol. 61(2), 225-247 (2002)
    • (2002) Theor. Popul. Biol. , vol.61 , Issue.2 , pp. 225-247
    • Rosenberg, N.A.1
  • 28
    • 84959788094 scopus 로고
    • Good and bad phenograms
    • Sackin, M.J.: Good and bad phenograms. Syst. Zool. 21, 225-226 (1972)
    • (1972) Syst. Zool. , vol.21 , pp. 225-226
    • Sackin, M.J.1
  • 29
    • 0034350321 scopus 로고    scopus 로고
    • Testing hybridization hypotheses based on incongruent gene trees
    • Sang, T., Zhong, Y.: Testing hybridization hypotheses based on incongruent gene trees. Syst. Biol. 49(3), 422-434 (2000)
    • (2000) Syst. Biol. , vol.49 , Issue.3 , pp. 422-434
    • Sang, T.1    Zhong, Y.2
  • 30
    • 84866458802 scopus 로고    scopus 로고
    • Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees
    • Stolzer, M., Lai, H., Xu, M., Sathaye, D., Vernot, B., Durand, D.: Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees. Bioinformatics 28(18), i409-i415 (2012)
    • (2012) Bioinformatics , vol.28 , Issue.18
    • Stolzer, M.1    Lai, H.2    Xu, M.3    Sathaye, D.4    Vernot, B.5    Durand, D.6
  • 31
    • 0024713112 scopus 로고
    • Gene genealogy in three related populations: Consistency probability between gene and population trees
    • Takahata, N.: Gene genealogy in three related populations: consistency probability between gene and population trees. Genetics 122(4), 957-966 (1989)
    • (1989) Genetics , vol.122 , Issue.4 , pp. 957-966
    • Takahata, N.1
  • 32
    • 46249126320 scopus 로고    scopus 로고
    • Duptree: A program for large-scale phylogenetic analyses using gene tree parsimony
    • Wehe, A., Bansal, M.S., Burleigh, J.G., Eulenstein, O.: Duptree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics 24(13), 1540-1541 (2008)
    • (2008) Bioinformatics , vol.24 , Issue.13 , pp. 1540-1541
    • Wehe, A.1    Bansal, M.S.2    Burleigh, J.G.3    Eulenstein, O.4
  • 33
    • 38549135938 scopus 로고    scopus 로고
    • Alignment uncertainty and genomic analysis
    • Wong, K.M., Suchard, M.A., Huelsenbeck, J.P.: Alignment uncertainty and genomic analysis. Science 319(5862), 473-476 (2008)
    • (2008) Science , vol.319 , Issue.5862 , pp. 473-476
    • Wong, K.M.1    Suchard, M.A.2    Huelsenbeck, J.P.3
  • 34
    • 0026031181 scopus 로고
    • Inferences of species phylogeny in relation to segregation of ancient polymorphisms
    • Wu, C.I.: Inferences of species phylogeny in relation to segregation of ancient polymorphisms. Genetics 127(2), 429-435 (1991)
    • (1991) Genetics , vol.127 , Issue.2 , pp. 429-435
    • Wu, C.I.1
  • 35
    • 84857687426 scopus 로고    scopus 로고
    • Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood
    • Wu, Y.: Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood. Evolution 66, 763-775 (2012)
    • (2012) Evolution , vol.66 , pp. 763-775
    • Wu, Y.1
  • 36
    • 79951575208 scopus 로고    scopus 로고
    • Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting
    • Yu, Y., Than, C., Degnan, J.H., Nakhleh, L.: Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting. Syst. Biol. 60(2), 138-149 (2011)
    • (2011) Syst. Biol. , vol.60 , Issue.2 , pp. 138-149
    • Yu, Y.1    Than, C.2    Degnan, J.H.3    Nakhleh, L.4
  • 37
    • 80052886059 scopus 로고    scopus 로고
    • From gene trees to species trees ii: Species tree inference by minimizing deep coalescence events
    • Zhang, L.X.: From gene trees to species trees ii: Species tree inference by minimizing deep coalescence events. IEEE-ACM Trans. Comput. Biol. Bioinform. 8(6), 1685-1691 (2011)
    • (2011) IEEE-ACM Trans. Comput. Biol. Bioinform. , vol.8 , Issue.6 , pp. 1685-1691
    • Zhang, L.X.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.