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Volumn 15, Issue 1, 2015, Pages

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

Author keywords

Gene duplication; Gene tree conflict; Incomplete lineage sorting; Phylogenomics; Transcriptome

Indexed keywords

ANGIOSPERM; ANIMAL; DATA SET; ECOLOGICAL MODELING; GENE EXPRESSION; GENOMICS; HOMOLOGY; HYBRIDIZATION; NOISE; PHYLOGENETICS; PHYLOGENY; RECONSTRUCTION; SOFTWARE;

EID: 84938602888     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/s12862-015-0423-0     Document Type: Article
Times cited : (316)

References (61)
  • 1
    • 42149157760 scopus 로고    scopus 로고
    • Broad phylogenomic sampling improves resolution of the animal tree of life
    • 1:CAS:528:DC%2BD1cXksFSju7k%3D 18322464 doi:10.1038/nature06614
    • Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, et al.Broad phylogenomic sampling improves resolution of the animal tree of life. Nature. 2008; 452(7188):745-9. doi: 10.1038/nature06614.
    • (2008) Nature , vol.452 , Issue.7188 , pp. 745-749
    • Dunn, C.W.1    Hejnol, A.2    Matus, D.Q.3    Pang, K.4    Browne, W.E.5    Smith, S.A.6
  • 2
    • 80053132393 scopus 로고    scopus 로고
    • Phylogenomics reveals deep molluscan relationships
    • 1:CAS:528:DC%2BC3MXhtFers7fE 4024475 21892190 doi:10.1038/nature10382
    • Kocot KM, Cannon JT, Todt C, Citarella MR, Kohn AB, Meyer A, et al. Phylogenomics reveals deep molluscan relationships. Nature. 2011; 477:452-6. doi: 10.1038/nature10382.
    • (2011) Nature , vol.477 , pp. 452-456
    • Kocot, K.M.1    Cannon, J.T.2    Todt, C.3    Citarella, M.R.4    Kohn, A.B.5    Meyer, A.6
  • 3
    • 83555166100 scopus 로고    scopus 로고
    • Resolving the evolutionary relationships of molluscs with phylogenomic tools
    • 1:CAS:528:DC%2BC3MXhtlOmsrnJ 22031330 doi:10.1038/nature10526
    • Smith SA, Wilson NG, Goetz FE, Feehery C, Andrade SCS, Rouse GW, et al.Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature. 2011; 480:364-7. doi: 10.1038/nature10526.
    • (2011) Nature , vol.480 , pp. 364-367
    • Smith, S.A.1    Wilson, N.G.2    Goetz, F.E.3    Feehery, C.4    Andrade, S.C.S.5    Rouse, G.W.6
  • 4
    • 84868678250 scopus 로고    scopus 로고
    • A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic lissamphibia
    • doi:10.1371/journal.pone.0048990
    • Fong JJ, Brown JM, Fujita MK, Boussau B. A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic lissamphibia. PLoS ONE. 2012; 7(11):48990. doi: 10.1371/journal.pone.0048990.
    • (2012) PLoS ONE , vol.7 , Issue.11
    • Fong, J.J.1    Brown, J.M.2    Fujita, M.K.3    Boussau, B.4
  • 5
    • 84886287737 scopus 로고    scopus 로고
    • Phylogenomics resolves evolutionary relationships among ants, bees, and wasps
    • 1:CAS:528:DC%2BC3sXhsFOltrzN 24094856 doi:10.1016/j.cub.2013.08.050
    • Johnson BR, Borowiec ML, Chiu JC, Lee EK, Atallah J, Ward PS. Phylogenomics resolves evolutionary relationships among ants, bees, and wasps. Curr Biol. 2013; 23:2058-062. doi: 10.1016/j.cub.2013.08.050.
    • (2013) Curr Biol , vol.23 , pp. 2058-2062
    • Johnson, B.R.1    Borowiec, M.L.2    Chiu, J.C.3    Lee, E.K.4    Atallah, J.5    Ward, P.S.6
  • 6
    • 84890056203 scopus 로고    scopus 로고
    • The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution
    • 3920664 24337300 doi:10.1126/science.1242592
    • Ryan JF, Pang K, Schnitzler CE, Nguyen AD, Moreland RT, Simmons DK, et al.The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science. 2013; 342:1242592. doi: 10.1126/science.1242592.
    • (2013) Science , vol.342
    • Ryan, J.F.1    Pang, K.2    Schnitzler, C.E.3    Nguyen, A.D.4    Moreland, R.T.5    Simmons, D.K.6
  • 7
    • 84883213635 scopus 로고    scopus 로고
    • Making the impossible possible: Rooting the tree of placental mammals
    • 1:CAS:528:DC%2BC3sXhtlals7bO 23813980 doi:10.1093/molbev/mst118
    • Teeling EC, Hedges SB. Making the impossible possible: Rooting the tree of placental mammals. Mol Biol Evol. 2013; 30(9):1999-2000. doi: 10.1093/molbev/mst118. http://mbe.oxfordjournals.org/content/30/9/1999.full.pdf+html.
    • (2013) Mol Biol Evol , vol.30 , Issue.9 , pp. 1999-2000
    • Teeling, E.C.1    Hedges, S.B.2
  • 8
    • 84917708482 scopus 로고    scopus 로고
    • Whole-genome analyses resolve early branches in the tree of life of modern birds
    • 1:CAS:528:DC%2BC2cXitVCgs7%2FK 4405904 25504713 doi:10.1126/science.1253451
    • Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, et al.Whole-genome analyses resolve early branches in the tree of life of modern birds. Science. 2014; 346(6215):1320-31. doi: 10.1126/science.1253451. http://www.sciencemag.org/content/346/6215/1320.full.pdf.
    • (2014) Science , vol.346 , Issue.6215 , pp. 1320-1331
    • Jarvis, E.D.1    Mirarab, S.2    Aberer, A.J.3    Li, B.4    Houde, P.5    Li, C.6
  • 9
    • 84909619344 scopus 로고    scopus 로고
    • Phylotranscriptomic analysis of the origin and early diversification of land plants
    • doi:10.1073/pnas.1323926111
    • Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, et al.Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc Natl Acad Sci. 2014; 111(45):4859-868. doi: 10.1073/pnas.1323926111. http://www.pnas.org/content/111/45/E4859.full.pdf+html.
    • (2014) Proc Natl Acad Sci , vol.111 , Issue.45 , pp. 4859-4868
    • Wickett, N.J.1    Mirarab, S.2    Nguyen, N.3    Warnow, T.4    Carpenter, E.5    Matasci, N.6
  • 10
    • 84919947905 scopus 로고    scopus 로고
    • Coalescent versus concatenation methods and the placement of amborella as sister to water lilies
    • 25077515 doi:10.1093/sysbio/syu055
    • Xi Z, Liu L, Rest JS, Davis CC. Coalescent versus concatenation methods and the placement of amborella as sister to water lilies. Syst Biol. 2014; 63(6):919-32. doi: 10.1093/sysbio/syu055. http://sysbio.oxfordjournals.org/content/63/6/919.full.pdf+html.
    • (2014) Syst Biol , vol.63 , Issue.6 , pp. 919-932
    • Xi, Z.1    Liu, L.2    Rest, J.S.3    Davis, C.C.4
  • 11
    • 84886742407 scopus 로고    scopus 로고
    • Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance
    • 3874668 24180377 doi:10.1186/1748-7188-8-28. 1210.2665
    • Chaudhary R, Burleigh JG, Fernández-Baca D. Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance. Algorithms Mol Biol. 2013; 8:28. doi: 10.1186/1748-7188-8-28. 1210.2665
    • (2013) Algorithms Mol Biol , vol.8 , pp. 28
    • Chaudhary, R.1    Burleigh, J.G.2    Fernández-Baca, D.3
  • 12
    • 84910635621 scopus 로고    scopus 로고
    • Phylogenomic interrogation of arachnida reveals systemic conflicts in phylogenetic signal
    • 25107551 doi:10.1093/molbev/msu235
    • Sharma PP, Kaluziak ST, Pérez-Porro AR, González VL, Hormiga G, Wheeler WC, et al.Phylogenomic interrogation of arachnida reveals systemic conflicts in phylogenetic signal. Mol Biol Evol. 2014; 31(11):2963-984. doi: 10.1093/molbev/msu235. http://mbe.oxfordjournals.org/content/31/11/2963.full.pdf+html.
    • (2014) Mol Biol Evol , vol.31 , Issue.11 , pp. 2963-2984
    • Sharma, P.P.1    Kaluziak, S.T.2    Pérez-Porro, A.R.3    González, V.L.4    Hormiga, G.5    Wheeler, W.C.6
  • 13
    • 57149095052 scopus 로고    scopus 로고
    • Dealing with incongruence in phylogenomic analyses
    • doi:10.1098/rstb.2008.0144
    • Galtier N, Daubin V. Dealing with incongruence in phylogenomic analyses. Philos Trans R Soc Lond B: Biol Sci. 2008; 363(1512):4023-029. doi: 10.1098/rstb.2008.0144.
    • (2008) Philos Trans R Soc Lond B: Biol Sci , vol.363 , Issue.1512 , pp. 4023-4029
    • Galtier, N.1    Daubin, V.2
  • 14
    • 33846839390 scopus 로고    scopus 로고
    • Bayesian estimation of concordance among gene trees
    • 17095535 doi:10.1093/molbev/msl170
    • Ané C, Larget B, Baum DA, Smith SD, Rokas A. Bayesian estimation of concordance among gene trees. Mol Biol Evol. 2007; 24:412-26. doi: 10.1093/molbev/msl170.
    • (2007) Mol Biol Evol , vol.24 , pp. 412-426
    • Ané, C.1    Larget, B.2    Baum, D.A.3    Smith, S.D.4    Rokas, A.5
  • 15
    • 70450233546 scopus 로고    scopus 로고
    • Estimating species trees: Methods of phylogenetic analysis when there is incongruence across genes
    • 20525600
    • Knowles LL. Estimating species trees: Methods of phylogenetic analysis when there is incongruence across genes. Syst Biol. 2009; 58(5):463-7.
    • (2009) Syst Biol , vol.58 , Issue.5 , pp. 463-467
    • Knowles, L.L.1
  • 16
    • 68049099068 scopus 로고    scopus 로고
    • Coalescent methods for estimating phylogenetic trees
    • 1:CAS:528:DC%2BD1MXptlyktrw%3D 19501178 doi:10.1016/j.ympev.2009.05.033
    • Liu L, Yu L, Kubatko L, Pearl DK, Edwards SV. Coalescent methods for estimating phylogenetic trees. Mol Phylogenet Evol. 2009; 53(1):320-8. doi: 10.1016/j.ympev.2009.05.033.
    • (2009) Mol Phylogenet Evol , vol.53 , Issue.1 , pp. 320-328
    • Liu, L.1    Yu, L.2    Kubatko, L.3    Pearl, D.K.4    Edwards, S.V.5
  • 17
    • 77958056150 scopus 로고    scopus 로고
    • Estimating species trees: An introduction to concepts and models
    • L.L. Knowles L.S. Kubatko, editors. Wiley-Blackwell Hoboken, New Jersey
    • Knowles LL, Kubatko LS. Estimating species trees: an introduction to concepts and models In: Knowles LL, Kubatko LS, editors. Estimating Species Trees: Practical and Theoretical Aspects. Hoboken, New Jersey: Wiley-Blackwell: 2010. p. 1-14.
    • (2010) Estimating Species Trees: Practical and Theoretical Aspects , pp. 1-14
    • Knowles, L.L.1    Kubatko, L.S.2
  • 18
    • 84866147332 scopus 로고    scopus 로고
    • Full modeling versus summarizing gene-tree uncertainty: Method choice and species-tree accuracy
    • 22835380 doi:10.1016/j.ympev.2012.07.004
    • Knowles LL, Lanier HC, Klimov PB, He Q. Full modeling versus summarizing gene-tree uncertainty: Method choice and species-tree accuracy. Mol Phylogenet Evol. 2012; 65(2):501-9. doi: 10.1016/j.ympev.2012.07.004.
    • (2012) Mol Phylogenet Evol , vol.65 , Issue.2 , pp. 501-509
    • Knowles, L.L.1    Lanier, H.C.2    Klimov, P.B.3    He, Q.4
  • 19
    • 84917708481 scopus 로고    scopus 로고
    • Statistical binning enables an accurate coalescent-based estimation of the avian tree
    • Mirarab S, Bayzid MS, Boussau B, Warnow T. Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science. 2014; 346(6215). doi: 10.1126/science.1250463. http://www.sciencemag.org/content/346/6215/1250463.full.pdf.
    • (2014) Science , vol.346 , Issue.6215
    • Mirarab, S.1    Bayzid, M.S.2    Boussau, B.3    Warnow, T.4
  • 20
    • 33846839295 scopus 로고    scopus 로고
    • Concordance trees, concordance factors, and the exploration of reticulate genealogy
    • Baum DA. Concordance trees, concordance factors, and the exploration of reticulate genealogy. Taxon. 2007; 56:417-26.
    • (2007) Taxon , vol.56 , pp. 417-426
    • Baum, D.A.1
  • 21
    • 78149256307 scopus 로고    scopus 로고
    • BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis
    • 1:CAS:528:DC%2BC3cXhsVSlt7fE 20861028 doi:10.1093/bioinformatics/btq539
    • Larget BR, Kotha SK, Dewey CN, Ané C. BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics. 2010; 26:2910-911. doi: 10.1093/bioinformatics/btq539.
    • (2010) Bioinformatics , vol.26 , pp. 2910-2911
    • Larget, B.R.1    Kotha, S.K.2    Dewey, C.N.3    Ané, C.4
  • 22
    • 84883482283 scopus 로고    scopus 로고
    • Naive binning improves phylogenomic analyses
    • 1:CAS:528:DC%2BC3sXhtlGmsLfM 23842808 doi:10.1093/bioinformatics/btt394
    • Bayzid MS, Warnow T. Naive binning improves phylogenomic analyses. Bioinformatics. 2013; 29:2277-284. doi: 10.1093/bioinformatics/btt394.
    • (2013) Bioinformatics , vol.29 , pp. 2277-2284
    • Bayzid, M.S.1    Warnow, T.2
  • 23
    • 84878113118 scopus 로고    scopus 로고
    • Inferring ancient divergences requires genes with strong phylogenetic signals
    • 1:CAS:528:DC%2BC3sXnvFSjtLc%3D 23657258 doi:10.1038/nature12130
    • Salichos L, Rokas A. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature. 2013; 497:327-1. doi: 10.1038/nature12130.
    • (2013) Nature , vol.497 , pp. 327-331
    • Salichos, L.1    Rokas, A.2
  • 24
    • 84873326063 scopus 로고    scopus 로고
    • Genome-scale coestimation of species and gene trees
    • 1:CAS:528:DC%2BC3sXitVemtL4%3D 3561873 23132911 doi:10.1101/gr.141978.112
    • Boussau B, Szollosi GJ, Duret L, Gouy M, Tannier E, Daubin V. Genome-scale coestimation of species and gene trees. Genome Res. 2013; 23:323-30. doi: 10.1101/gr.141978.112.
    • (2013) Genome Res , vol.23 , pp. 323-330
    • Boussau, B.1    Szollosi, G.J.2    Duret, L.3    Gouy, M.4    Tannier, E.5    Daubin, V.6
  • 25
    • 84898641369 scopus 로고    scopus 로고
    • Novel information theory-based measures for quantifying incongruence among phylogenetic trees
    • 1:CAS:528:DC%2BC2cXmvFCitLs%3D 24509691 doi:10.1093/molbev/msu061
    • Salichos L, Stamatakis A, Rokas A. Novel information theory-based measures for quantifying incongruence among phylogenetic trees. Mol Biol Evol. 2014; 31:1261-1271. doi: 10.1093/molbev/msu061.
    • (2014) Mol Biol Evol , vol.31 , pp. 1261-1271
    • Salichos, L.1    Stamatakis, A.2    Rokas, A.3
  • 26
    • 84910656190 scopus 로고    scopus 로고
    • Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: Improving accuracy and matrix occupancy for phylogenomics
    • 4209138 25158799 doi:10.1093/molbev/msu245
    • Yang Y, Smith SA. Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: Improving accuracy and matrix occupancy for phylogenomics. Mol Biol Evol. 2014; 31:3081-092. doi: 10.1093/molbev/msu245.
    • (2014) Mol Biol Evol , vol.31 , pp. 3081-3092
    • Yang, Y.1    Smith, S.A.2
  • 27
    • 84857090152 scopus 로고    scopus 로고
    • Maximum likelihood models and algorithms for gene tree evolution with duplications and losses
    • Gorecki P, Burleigh GJ, Eulenstein O. Maximum likelihood models and algorithms for gene tree evolution with duplications and losses. BMC Bioinformatics. 2011; 12(Supp 1):1-15. doi: 10.1186/1471-2105-12-S1-S15.
    • (2011) BMC Bioinformatics , vol.12 , pp. 1-15
    • Gorecki, P.1    Burleigh, G.J.2    Eulenstein, O.3
  • 28
    • 84859546516 scopus 로고    scopus 로고
    • Unified modeling of gene duplication, loss, and coalescence using a locus tree
    • 1:CAS:528:DC%2BC38Xlt1egtrg%3D 3317157 22271778 doi:10.1101/gr.123901.111
    • Rasmussen MD, Kellis M. Unified modeling of gene duplication, loss, and coalescence using a locus tree. Genome Res. 2012; 22(4):755-65. doi: 10.1101/gr.123901.111. http://genome.cshlp.org/content/22/4/755.full.pdf+html.
    • (2012) Genome Res , vol.22 , Issue.4 , pp. 755-765
    • Rasmussen, M.D.1    Kellis, M.2
  • 29
    • 84877597619 scopus 로고    scopus 로고
    • Optimizing de novo assembly of short-read RNA-seq data for phylogenomics
    • 1:CAS:528:DC%2BC3sXptlyiurk%3D 3663818 23672450 doi:10.1186/1471-2164-14-328
    • Yang Y, Smith SA. Optimizing de novo assembly of short-read RNA-seq data for phylogenomics. BMC Genomics. 2013; 14:328. doi: 10.1186/1471-2164-14-328.
    • (2013) BMC Genomics , vol.14 , pp. 328
    • Yang, Y.1    Smith, S.A.2
  • 30
    • 84874372267 scopus 로고    scopus 로고
    • Family-level divergences in the stinging wasps (Hymenoptera: Aculeata), with correlations to angiosperm diversification
    • doi:10.1007/s11692-012-9189-0
    • Wilson JS, von Dohlen CD, Forister ML, Pitts JP. Family-level divergences in the stinging wasps (Hymenoptera: Aculeata), with correlations to angiosperm diversification. Evol Biol. 2013; 40:101-7. doi: 10.1007/s11692-012-9189-0.
    • (2013) Evol Biol , vol.40 , pp. 101-107
    • Wilson, J.S.1    Von Dohlen, C.D.2    Forister, M.L.3    Pitts, J.P.4
  • 31
    • 70350218974 scopus 로고    scopus 로고
    • An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III
    • doi:10.1111/j.1095-8339.2009.00996.x
    • Bremer B, Bremer K, Chase MW, Fay MF, Reveal JL, Bailey LH, et al.An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot J Linn Soc. 2009; 161:105-21. doi: 10.1111/j.1095-8339.2009.00996.x.
    • (2009) Bot J Linn Soc , vol.161 , pp. 105-121
    • Bremer, B.1    Bremer, K.2    Chase, M.W.3    Fay, M.F.4    Reveal, J.L.5    Bailey, L.H.6
  • 32
    • 77955991477 scopus 로고    scopus 로고
    • The age and diversification of the angiosperms re-revisited
    • 21616882 doi:10.3732/ajb.0900346
    • Bell CD, Soltis DE, Soltis PS. The age and diversification of the angiosperms re-revisited. Am J Bot. 2010; 97:1296-303. doi: 10.3732/ajb.0900346.
    • (2010) Am J Bot , vol.97 , pp. 1296-1303
    • Bell, C.D.1    Soltis, D.E.2    Soltis, P.S.3
  • 33
    • 77949494249 scopus 로고    scopus 로고
    • Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots
    • 1:CAS:528:DC%2BC3cXjs1emurc%3D 2842043 20176954 doi:10.1073/pnas.0907801107
    • Moore MJ, Soltis PS, Bell CD, Burleigh JG, Soltis DE. Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots. Proc Natl Acad Sci U S A. 2010; 107:4623-628. doi: 10.1073/pnas.0907801107.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 4623-4628
    • Moore, M.J.1    Soltis, P.S.2    Bell, C.D.3    Burleigh, J.G.4    Soltis, D.E.5
  • 35
    • 0036188663 scopus 로고    scopus 로고
    • Molecular phylogenetics of Caryophyllales based on nuclear 18S rDNA and plastid rbcL, atpB, and matK DNA sequences
    • 21669721 doi:10.3732/ajb.89.1.132
    • Cuénoud P, Savolainen V, Chatrou LW, Powell M, Grayer RJ, Chase MW. Molecular phylogenetics of Caryophyllales based on nuclear 18S rDNA and plastid rbcL, atpB, and matK DNA sequences. Am J Bot. 2002; 89:132-44. doi: 10.3732/ajb.89.1.132.
    • (2002) Am J Bot , vol.89 , pp. 132-144
    • Cuénoud, P.1    Savolainen, V.2    Chatrou, L.W.3    Powell, M.4    Grayer, R.J.5    Chase, M.W.6
  • 36
    • 79955538408 scopus 로고    scopus 로고
    • Caryophyllales phylogenetics: Disentangling Phytolaccaceae and Molluginaceae and description of Microteaceae as a new isolated family
    • doi:10.3372/wi.39.39201
    • Schäferhoff B, Müller KF, Borsch T. Caryophyllales phylogenetics: disentangling Phytolaccaceae and Molluginaceae and description of Microteaceae as a new isolated family. Willdenowia. 2009; 39:209-28. doi: 10.3372/wi.39.39201.
    • (2009) Willdenowia , vol.39 , pp. 209-228
    • Schäferhoff, B.1    Müller, K.F.2    Borsch, T.3
  • 37
    • 79957676298 scopus 로고    scopus 로고
    • Contemporaneous and recent radiations of the world's major succulent plant lineages
    • 1:CAS:528:DC%2BC3MXmsF2jt7k%3D 3100969 21536881 doi:10.1073/pnas.1100628108
    • Arakaki M, Christin PA, Nyffeler R, Lendel A, Eggli U, Ogburn RM, et al.Contemporaneous and recent radiations of the world's major succulent plant lineages. Proc Natl Acad Sci U S A. 2011; 108:8379-384. doi: 10.1073/pnas.1100628108.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 8379-8384
    • Arakaki, M.1    Christin, P.A.2    Nyffeler, R.3    Lendel, A.4    Eggli, U.5    Ogburn, R.M.6
  • 38
    • 70349169872 scopus 로고    scopus 로고
    • Phylogeny of the Caryophyllales Sensu Lato: Revisiting Hypotheses on Pollination Biology and Perianth Differentiation in the Core Caryophyllales
    • doi:10.1086/597785
    • Brockington SF, Alexandre R, Ramdial J, Moore MJ, Crawley S, Dhingra A, et al.Phylogeny of the Caryophyllales Sensu Lato: Revisiting Hypotheses on Pollination Biology and Perianth Differentiation in the Core Caryophyllales. Int J Plant Sci. 2009; 170:627-43. doi: 10.1086/597785.
    • (2009) Int J Plant Sci , vol.170 , pp. 627-643
    • Brockington, S.F.1    Alexandre, R.2    Ramdial, J.3    Moore, M.J.4    Crawley, S.5    Dhingra, A.6
  • 39
    • 79955778297 scopus 로고    scopus 로고
    • Complex pigment evolution in the Caryophyllales
    • 1:CAS:528:DC%2BC3MXot1Crtbc%3D 21714182 doi:10.1111/j.1469-8137.2011.03687.x
    • Brockington SF, Walker RH, Glover BJ, Soltis PS, Soltis DE. Complex pigment evolution in the Caryophyllales. New Phytologist. 2011; 190:854-64. doi: 10.1111/j.1469-8137.2011.03687.x.
    • (2011) New Phytologist , vol.190 , pp. 854-864
    • Brockington, S.F.1    Walker, R.H.2    Glover, B.J.3    Soltis, P.S.4    Soltis, D.E.5
  • 41
    • 84856214128 scopus 로고    scopus 로고
    • Impact of missing data, gene choice, and taxon sampling on phylogenetic reconstruction: The Caryophyllales (angiosperms)
    • doi:10.1007/s00606-011-0544-x
    • Crawley SS, Hilu KW. Impact of missing data, gene choice, and taxon sampling on phylogenetic reconstruction: The Caryophyllales (angiosperms). Plant Syst Evol. 2012; 298:297-312. doi: 10.1007/s00606-011-0544-x.
    • (2012) Plant Syst Evol , vol.298 , pp. 297-312
    • Crawley, S.S.1    Hilu, K.W.2
  • 42
    • 84965099240 scopus 로고    scopus 로고
    • Dissecting molecular evolution in the highly diverse plant clade caryophyllales using transcriptome sequencing
    • Yang Y, Moore MJ, Brockington SF, Soltis DE, Wong GK-S, Carpenter EJ, et al.Dissecting molecular evolution in the highly diverse plant clade caryophyllales using transcriptome sequencing. Mol Biol Evol. 2015. doi: 10.1093/molbev/msv081. http://mbe.oxfordjournals.org/content/early/2015/04/22/molbev.msv081.full.pdf+html.
    • (2015) Mol Biol Evol
    • Yang, Y.1    Moore, M.J.2    Brockington, S.F.3    Soltis, D.E.4    Wong, G.K.-S.5    Carpenter, E.J.6
  • 43
    • 33750460281 scopus 로고    scopus 로고
    • Insights into social insects from the genome of the honeybee Apis mellifera
    • 1:CAS:528:DC%2BD28XhtFaksrjK doi:10.1038/nature05260
    • Weinstock GM, Robinson GE, Gibbs RA, Worley KC, Evans JD, Maleszka R, et al.Insights into social insects from the genome of the honeybee Apis mellifera. Nature. 2006; 443:931-49. doi: 10.1038/nature05260.
    • (2006) Nature , vol.443 , pp. 931-949
    • Weinstock, G.M.1    Robinson, G.E.2    Gibbs, R.A.3    Worley, K.C.4    Evans, J.D.5    Maleszka, R.6
  • 44
    • 77956109363 scopus 로고    scopus 로고
    • Genomic comparison of the ants Camponotus floridanus and Harpegnathos saltator
    • 1:CAS:528:DC%2BC3cXhtVGrt7bF 3772619 20798317 doi:10.1126/science.1192428
    • Bonasio R, Zhang G, Ye C, Mutti NS, Fang X, Qin N, et al.Genomic comparison of the ants Camponotus floridanus and Harpegnathos saltator. Science. 2010; 329:1068-71. doi: 10.1126/science.1192428.
    • (2010) Science , vol.329 , pp. 1068-1071
    • Bonasio, R.1    Zhang, G.2    Ye, C.3    Mutti, N.S.4    Fang, X.5    Qin, N.6
  • 45
    • 74549184089 scopus 로고    scopus 로고
    • The Nasonia Genome Working Group: Functional and evolutionary insights from the genomes of three parasitoid Nasonia species
    • 1:CAS:528:DC%2BC3cXktlWlug%3D%3D 20075255 doi:10.1126/science.1178028
    • Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK. The Nasonia Genome Working Group: Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science. 2010; 327:343-8. doi: 10.1126/science.1178028.
    • (2010) Science , vol.327 , pp. 343-348
    • Werren, J.H.1    Richards, S.2    Desjardins, C.A.3    Niehuis, O.4    Gadau, J.5    Colbourne, J.K.6
  • 46
    • 79955002712 scopus 로고    scopus 로고
    • Draft genome of the red harvester ant Pogonomyrmex barbatus
    • 1:CAS:528:DC%2BC3MXkvVCjt7s%3D 3078412 21282651 doi:10.1073/pnas.1007901108
    • Smith CR, Smith CD, Robertson HM, Helmkampf M, Zimin A, Yandell M, et al.Draft genome of the red harvester ant Pogonomyrmex barbatus. Proc Natl Acad Sci U S A. 2011; 108:5667-672. doi: 10.1073/pnas.1007901108.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 5667-5672
    • Smith, C.R.1    Smith, C.D.2    Robertson, H.M.3    Helmkampf, M.4    Zimin, A.5    Yandell, M.6
  • 47
    • 79954986915 scopus 로고    scopus 로고
    • Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile)
    • 1:CAS:528:DC%2BC3MXkvVCju7s%3D 3078359 21282631 doi:10.1073/pnas.1008617108
    • Smith CD, Zimin A, Holt C, Abouheif E, Benton R, Cash E, et al.Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). Proc Natl Acad Sci U S A. 2011; 108:5673-678. doi: 10.1073/pnas.1008617108.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 5673-5678
    • Smith, C.D.1    Zimin, A.2    Holt, C.3    Abouheif, E.4    Benton, R.5    Cash, E.6
  • 48
    • 84890455442 scopus 로고    scopus 로고
    • The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes
    • doi:10.1186/gb-2013-14-12-r142
    • Kocher SD, Li C, Yang W, Tan H, Yi SV, Yang X, et al.The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes. Genome Biol. 2013; 14:142. doi: 10.1186/gb-2013-14-12-r142.
    • (2013) Genome Biol , vol.14 , pp. 142
    • Kocher, S.D.1    Li, C.2    Yang, W.3    Tan, H.4    Yi, S.V.5    Yang, X.6
  • 49
    • 84938673045 scopus 로고    scopus 로고
    • PhD thesis, University of Utrecht
    • van Dongen S. Graph clustering: PhD thesis, University of Utrecht; 2000.
    • (2000) Graph Clustering
    • Van Dongen, S.1
  • 50
    • 84875619226 scopus 로고    scopus 로고
    • MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
    • 1:CAS:528:DC%2BC3sXksFWisLc%3D 3603318 23329690 doi:10.1093/molbev/mst010
    • Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol Biol Evol. 2013; 30:772-80. doi: 10.1093/molbev/mst010.
    • (2013) Mol Biol Evol , vol.30 , pp. 772-780
    • Katoh, K.1    Standley, D.M.2
  • 51
    • 84555194934 scopus 로고    scopus 로고
    • SATe-II: Very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees
    • 22139466 doi:10.1093/sysbio/syr095
    • Liu K, Warnow TJ, Holder MT, Nelesen SM, Yu J, Stamatakis AP, et al.SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Syst Biol. 2012; 61:90-106. doi: 10.1093/sysbio/syr095.
    • (2012) Syst Biol , vol.61 , pp. 90-106
    • Liu, K.1    Warnow, T.J.2    Holder, M.T.3    Nelesen, S.M.4    Yu, J.5    Stamatakis, A.P.6
  • 52
    • 84899553363 scopus 로고    scopus 로고
    • RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
    • 1:CAS:528:DC%2BC2cXmvFCjsbc%3D 3998144 24451623 doi:10.1093/bioinformatics/btu033 bioinformatics/btu033
    • Stamatakis A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014; 30:1312-1313. doi: 10.1093/bioinformatics/btu033 bioinformatics/btu033
    • (2014) Bioinformatics , vol.30 , pp. 1312-1313
    • Stamatakis, A.1
  • 53
    • 65649131928 scopus 로고    scopus 로고
    • Gene tree discordance, phylogenetic inference and the multispecies coalescent
    • 19307040 doi:10.1016/j.tree.2009.01.009
    • Degnan JH, Rosenberg NA. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol. 2009; 24:332-40. doi: 10.1016/j.tree.2009.01.009.
    • (2009) Trends Ecol Evol , vol.24 , pp. 332-340
    • Degnan, J.H.1    Rosenberg, N.A.2
  • 54
    • 13244292527 scopus 로고    scopus 로고
    • Gene tree distributions under the coalescent process
    • 15792224 doi:10.1111/j.0014-3820.2005.tb00891.x
    • Degnan JH, Salter LA. Gene tree distributions under the coalescent process. Evolution. 2005; 59(1):24-37. doi: 10.1111/j.0014-3820.2005.tb00891.x.
    • (2005) Evolution , vol.59 , Issue.1 , pp. 24-37
    • Degnan, J.H.1    Salter, L.A.2
  • 55
    • 84870458929 scopus 로고    scopus 로고
    • treepl: Divergence time estimation using penalized likelihood for large phylogenies
    • 1:CAS:528:DC%2BC38XhsFWktrrO 22908216 doi:10.1093/bioinformatics/bts492
    • Smith SA, O'Meara BC. treepl: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics. 2012; 28(20):2689-690. doi: 10.1093/bioinformatics/bts492. http://bioinformatics.oxfordjournals.org/content/28/20/2689.full.pdf+html.
    • (2012) Bioinformatics , vol.28 , Issue.20 , pp. 2689-2690
    • Smith, S.A.1    O'Meara, B.C.2
  • 56
    • 3042672020 scopus 로고    scopus 로고
    • Functional annotation of the Arabidopsis genome using controlled vocabularies
    • 1:CAS:528:DC%2BD2cXltlKjurg%3D 514112 15173566 doi:10.1104/pp.104.040071
    • Berardini TZ, Mundodi S, Reiser L, Huala E, Garcia-Hernandez M, Zhang P, et al.Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol. 2004; 135:745-55. doi: 10.1104/pp.104.040071.
    • (2004) Plant Physiol , vol.135 , pp. 745-755
    • Berardini, T.Z.1    Mundodi, S.2    Reiser, L.3    Huala, E.4    Garcia-Hernandez, M.5    Zhang, P.6
  • 57
    • 84891808813 scopus 로고    scopus 로고
    • FlyBase 102-advanced approaches to interrogating FlyBase
    • doi:10.1093/nar/gkt1092
    • St Pierre SE, Ponting L, Stefancsik R, McQuilton P. FlyBase 102-advanced approaches to interrogating FlyBase. Nucleic Acids Res. 2014; 42:780-8. doi: 10.1093/nar/gkt1092.
    • (2014) Nucleic Acids Res , vol.42 , pp. 780-788
    • St Pierre, S.E.1    Ponting, L.2    Stefancsik, R.3    McQuilton, P.4
  • 58
    • 51349098340 scopus 로고    scopus 로고
    • Phylonet: A software package for analyzing and reconstructing reticulate evolutionary relationships
    • 2533029 18662388 doi:10.1186/1471-2105-9-322
    • Than C, Ruths D, Nakhleh L. Phylonet: a software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinformatics. 2008; 9(1):322. doi: 10.1186/1471-2105-9-322.
    • (2008) BMC Bioinformatics , vol.9 , Issue.1 , pp. 322
    • Than, C.1    Ruths, D.2    Nakhleh, L.3
  • 59
    • 70349425459 scopus 로고    scopus 로고
    • Estimating species phylogenies using coalescence times among sequences
    • 1:CAS:528:DC%2BD1MXhsVCisbjN 20525601 doi:10.1093/sysbio/syp031
    • Liu L, Yu L, Pearl DK, Edwards SV. Estimating species phylogenies using coalescence times among sequences. Syst Biol. 2009; 58(5):468-77. doi: 10.1093/sysbio/syp031. http://sysbio.oxfordjournals.org/content/58/5/468.full.pdf+html.
    • (2009) Syst Biol , vol.58 , Issue.5 , pp. 468-477
    • Liu, L.1    Yu, L.2    Pearl, D.K.3    Edwards, S.V.4
  • 60
    • 84922482181 scopus 로고    scopus 로고
    • Extensive introgression in a malaria vector species complex revealed by phylogenomics
    • Fontaine MC, Pease JB, Steele A, Waterhouse RM, Neafsey DE, Sharakhov IV, et al.Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science. 6217; 347. doi: 10.1126/science.1258524. http://www.sciencemag.org/content/347/6217/1258524.full.pdf.
    • Science , vol.6217 , pp. 347
    • Fontaine, M.C.1    Pease, J.B.2    Steele, A.3    Waterhouse, R.M.4    Neafsey, D.E.5    Sharakhov, I.V.6
  • 61
    • 84906251283 scopus 로고    scopus 로고
    • Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3
    • 1:CAS:528:DC%2BC2cXhtl2gur3P 24721692 doi:10.1093/sysbio/syu027
    • Zwickl DJ, Stein JC, Wing RA, Ware D, Sanderson MJ. Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3. Syst Biol. 2014; 63:645-59. doi: 10.1093/sysbio/syu027.
    • (2014) Syst Biol , vol.63 , pp. 645-659
    • Zwickl, D.J.1    Stein, J.C.2    Wing, R.A.3    Ware, D.4    Sanderson, M.J.5


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