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Volumn 64, Issue 5, 2015, Pages 792-808

Species-level phylogeny and polyploid relationships in Hordeum (Poaceae) inferred by next-generation sequencing and in silico cloning of multiple nuclear loci

Author keywords

Evolution; Hordeum; In silico cloning; Multispecies coalescent; Nuclear single copy genes; Phylogeny; Polyploidy; Systematics

Indexed keywords

CHLOROPLAST DNA;

EID: 84954175087     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syv035     Document Type: Article
Times cited : (86)

References (95)
  • 2
    • 0344613211 scopus 로고    scopus 로고
    • Ribosomal ITS sequences and plant phylogenetic inference
    • Álvarez I., Wendel J.F. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogenet. Evol. 29: 417-434.
    • (2003) Mol. Phylogenet. Evol. , vol.29 , pp. 417-434
    • Álvarez, I.1    Wendel, J.F.2
  • 4
    • 33846839295 scopus 로고    scopus 로고
    • Concordance trees, concordance factors, and the exploration of reticulate genealogy
    • Baum D.A. 2007. Concordance trees, concordance factors, and the exploration of reticulate genealogy. Taxon 56: 417-426.
    • (2007) Taxon , vol.56 , pp. 417-426
    • Baum, D.A.1
  • 5
    • 1942511467 scopus 로고    scopus 로고
    • Phylogenetic analysis of Hordeum (Poaceae) as inferred by nuclear rDNA ITS sequences
    • Blattner F.R. 2004. Phylogenetic analysis of Hordeum (Poaceae) as inferred by nuclear rDNA ITS sequences. Mol. Phylogenet. Evol. 33: 289-299.
    • (2004) Mol. Phylogenet. Evol. , vol.33 , pp. 289-299
    • Blattner, F.R.1
  • 6
    • 33645094639 scopus 로고    scopus 로고
    • Multiple intercontinental dispersals shaped the distribution area of Hordeum (Poaceae
    • Blattner F.R. 2006. Multiple intercontinental dispersals shaped the distribution area of Hordeum (Poaceae). New Phytol. 169: 603-614.
    • (2006) New Phytol. , vol.169 , pp. 603-614
    • Blattner, F.R.1
  • 7
    • 72549119205 scopus 로고    scopus 로고
    • Progress in phylogenetic analysis and a new infrageneric classification of the barley genus Hordeum (Poaceae: Triticeae
    • Blattner F.R. 2009. Progress in phylogenetic analysis and a new infrageneric classification of the barley genus Hordeum (Poaceae: Triticeae). Breed. Sci. 59: 471-480.
    • (2009) Breed. Sci. , vol.59 , pp. 471-480
    • Blattner, F.R.1
  • 8
    • 84920182495 scopus 로고    scopus 로고
    • Rapid radiation in the barley genus Hordeum (Poaceae) during the Pleistocene in the Americas
    • In: Glaubrecht M., editor Berlin, Heidelberg: Springer
    • Blattner F.R., Pleines T., Jakob S.S. 2010. Rapid radiation in the barley genus Hordeum (Poaceae) during the Pleistocene in the Americas. In: Glaubrecht M., editor. Evolution in action. Berlin, Heidelberg: Springer. p. 17-33.
    • (2010) Evolution in Action , pp. 17-33
    • Blattner, F.R.1    Pleines, T.2    Jakob, S.S.3
  • 10
    • 84859128656 scopus 로고    scopus 로고
    • Progenitor-derivative relationships of Hordeum polyploids (Poaceae, Triticeae) inferred from sequences of TOPO6, a nuclear low-copy gene region
    • Brassac J., Jakob S.S., Blattner F.R. 2012. Progenitor-derivative relationships of Hordeum polyploids (Poaceae, Triticeae) inferred from sequences of TOPO6, a nuclear low-copy gene region. PLoS ONE 7: E33808.
    • (2012) PLoS ONE , vol.7 , pp. e33808
    • Brassac, J.1    Jakob, S.S.2    Blattner, F.R.3
  • 11
    • 0000702887 scopus 로고
    • Recurrent formation and polyphyly of Nordic polyploids in Draba (Brassicaceae
    • Brochmann C., Soltis P.S., Soltis D.E. 1992. Recurrent formation and polyphyly of Nordic polyploids in Draba (Brassicaceae). Am. J. Bot. 79: 673-688.
    • (1992) Am. J. Bot. , vol.79 , pp. 673-688
    • Brochmann, C.1    Soltis, P.S.2    Soltis, D.E.3
  • 13
    • 84889839528 scopus 로고    scopus 로고
    • The evolutionary history of sea barley (Hordeum marinum) revealed by comparative physical mapping of repetitive DNA
    • Carmona A., Friero E., Bustos A. de, Jouve N., Cuadrado A. 2013. The evolutionary history of sea barley (Hordeum marinum) revealed by comparative physical mapping of repetitive DNA. Ann. Bot. 112: 1845-1855.
    • (2013) Ann. Bot. , vol.112 , pp. 1845-1855
    • Carmona, A.1    Friero, E.2    Bustos, A.3    Jouve, N.4    Cuadrado, A.5
  • 14
    • 79955380843 scopus 로고    scopus 로고
    • Comparing two Bayesian methods for gene tree/species tree reconstruction: Simulations with incomplete lineage sorting and horizontal gene transfer
    • Chung Y., Ané C. 2011. Comparing two Bayesian methods for gene tree/species tree reconstruction: Simulations with incomplete lineage sorting and horizontal gene transfer. Syst. Biol. 60: 261-275.
    • (2011) Syst. Biol. , vol.60 , pp. 261-275
    • Chung, Y.1    Ané, C.2
  • 15
    • 0031741723 scopus 로고    scopus 로고
    • The effect of Quaternary climatic changes on plant distribution and evolution
    • Comes H.P., Kadereit J.W. 1998. The effect of Quaternary climatic changes on plant distribution and evolution. Trends Plant Sci. 3: 432-438.
    • (1998) Trends Plant Sci. , vol.3 , pp. 432-438
    • Comes, H.P.1    Kadereit, J.W.2
  • 16
    • 84864453108 scopus 로고    scopus 로고
    • JModelTest 2: More models, newheuristics and parallel computing.Nat
    • Darriba D., Taboada G.L., Doallo R., Posada D. 2012. jModelTest 2: More models, newheuristics and parallel computing.Nat. Methods 9: 772-772.
    • (2012) Methods , vol.9 , pp. 772
    • Darriba, D.1    Taboada, G.L.2    Doallo, R.3    Posada, D.4
  • 17
    • 65649131928 scopus 로고    scopus 로고
    • Gene tree discordance, phylogenetic inference and the multispecies coalescent
    • Degnan J.H., Rosenberg N.A. 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
  • 18
    • 0001661219 scopus 로고
    • ChloroplastDNAvariation and the phylogeny of Hordeum (Poaceae
    • Doebley J., Bothmer R. von, Larson S. 1992. ChloroplastDNAvariation and the phylogeny of Hordeum (Poaceae). Am. J. Bot. 79: 576-584.
    • (1992) Am. J. Bot. , vol.79 , pp. 576-584
    • Doebley, J.1    Bothmer, R.2    Larson, S.3
  • 20
    • 38649110663 scopus 로고    scopus 로고
    • BEAST: Bayesian evolutionary analysis by sampling trees
    • Drummond A.J., Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7: 214.
    • (2007) BMC Evol. Biol. , vol.7 , pp. 214
    • Drummond, A.J.1    Rambaut, A.2
  • 21
    • 77956488734 scopus 로고    scopus 로고
    • Bayesian random local clocks, or one rate to rule them all
    • Drummond A.J., Suchard M.A. 2010. Bayesian random local clocks, or one rate to rule them all. BMC Biol. 8: 114.
    • (2010) BMC Biol. , vol.8 , pp. 114
    • Drummond, A.J.1    Suchard, M.A.2
  • 23
    • 58249100073 scopus 로고    scopus 로고
    • Is a new and general theory of molecular systematics emerging?
    • Edwards S.V. 2009. Is a new and general theory of molecular systematics emerging? Evolution 63: 1-19.
    • (2009) Evolution , vol.63 , pp. 1-19
    • Edwards, S.V.1
  • 25
    • 79953122203 scopus 로고    scopus 로고
    • A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses
    • Griffin P., Robin C., Hoffmann A. 2011. A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses. BMC Biol. 9: 19.
    • (2011) BMC Biol. , vol.9 , pp. 19
    • Griffin, P.1    Robin, C.2    Hoffmann, A.3
  • 26
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon S., Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52: 696-704.
    • (2003) Syst. Biol. , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 27
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa M., Kishino H., Yano T. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22: 160-174.
    • (1985) J. Mol. Evol. , vol.22 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 28
    • 77249086587 scopus 로고    scopus 로고
    • Bayesian inference of species trees from multilocus data
    • Heled J., DrummondA.J. 2010. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 27: 570-580.
    • (2010) Mol. Biol. Evol. , vol.4 , Issue.27 , pp. 570-580
    • Heled, J.1    Drummond, A.J.2
  • 29
    • 0029860602 scopus 로고    scopus 로고
    • Some genetic consequences of ice ages, and their role in divergence and speciation
    • Hewitt G.M. 1996. Some genetic consequences of ice ages, and their role in divergence and speciation. Biol. J. Linn. Soc. 58: 247-276.
    • (1996) Biol. J. Linn. Soc. , vol.58 , pp. 247-276
    • Hewitt, G.M.1
  • 30
    • 11444256350 scopus 로고    scopus 로고
    • Revealing unknownor extinct lineages within Isoëtes (Isoëtaceae) using DNA sequences from hybrids
    • Hoot S.B.,NapierN.S., TaylorW.C. 2004. Revealing unknownor extinct lineages within Isoëtes (Isoëtaceae) using DNA sequences from hybrids. Am. J. Bot. 91: 899-904.
    • (2004) Am. J. Bot. , vol.91 , pp. 899-904
    • Hoot S.B.NapierN., S.1    Taylor, W.C.2
  • 31
    • 0030902563 scopus 로고    scopus 로고
    • Phylogenetic methods come of age: Testing hypotheses in an evolutionary context
    • Huelsenbeck J.P., Rannala B. 1997. Phylogenetic methods come of age: Testing hypotheses in an evolutionary context. Science 276: 227-232.
    • (1997) Science , vol.276 , pp. 227-232
    • Huelsenbeck, J.P.1    Rannala, B.2
  • 32
    • 58549112370 scopus 로고    scopus 로고
    • Localization of anchor loci representing five hundred annotated rice genes to wheat chromosomes using PLUG markers
    • Ishikawa G., Nakamura T., Ashida T., Saito M., Nasuda S., Endo T.R., Wu J., Matsumoto T. 2009. Localization of anchor loci representing five hundred annotated rice genes to wheat chromosomes using PLUG markers. Theor. Appl. Genet. 118: 499-514.
    • (2009) Theor. Appl. Genet. , vol.118 , pp. 499-514
    • Ishikawa, G.1    Nakamura, T.2    Ashida, T.3    Saito, M.4    Nasuda, S.5    Endo, T.R.6    Wu, J.7    Matsumoto, T.8
  • 33
    • 34347386048 scopus 로고    scopus 로고
    • PCRbased landmark unique gene (PLUG) markers effectively assign homoeologous wheat genes toA, B andDgenomes
    • Ishikawa G., Yonemaru J., Saito M., Nakamura T. 2007. PCRbased landmark unique gene (PLUG) markers effectively assign homoeologous wheat genes toA, B andDgenomes.BMCGenomics 8: 135.
    • (2007) BMCGenomics , vol.8 , pp. 135
    • Ishikawa, G.1    Yonemaru, J.2    Saito, M.3    Nakamura, T.4
  • 34
    • 33748073420 scopus 로고    scopus 로고
    • A chloroplast genealogy of Hordeum (Poaceae): Long-term persisting haplotypes, incomplete lineage sorting, regional extinction, and the consequences for phylogenetic inference
    • Jakob S.S., Blattner F.R. 2006. A chloroplast genealogy of Hordeum (Poaceae): Long-term persisting haplotypes, incomplete lineage sorting, regional extinction, and the consequences for phylogenetic inference. Mol. Biol. Evol. 23: 1602-1612.
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 1602-1612
    • Jakob, S.S.1    Blattner, F.R.2
  • 35
    • 77949790447 scopus 로고    scopus 로고
    • Two extinct diploid progenitors were involved in allopolyploid formation in the Hordeum murinum (Poaceae: Triticeae) taxon complex
    • Jakob S.S., Blattner F.R. 2010. Two extinct diploid progenitors were involved in allopolyploid formation in the Hordeum murinum (Poaceae: Triticeae) taxon complex. Mol. Phylogenet. Evol. 55: 650-659.
    • (2010) Mol. Phylogenet. Evol. , vol.55 , pp. 650-659
    • Jakob, S.S.1    Blattner, F.R.2
  • 36
    • 77949841155 scopus 로고    scopus 로고
    • Population demography influences climatic niche evolution: Evidence from diploid American Hordeum species (Poaceae
    • Jakob S.S., Heibl C., Rödder D., Blattner F.R. 2010. Population demography influences climatic niche evolution: Evidence from diploid American Hordeum species (Poaceae). Mol. Ecol. 19: 1423-1438.
    • (2010) Mol. Ecol. , vol.19 , pp. 1423-1438
    • Jakob, S.S.1    Heibl, C.2    Rödder, D.3    Blattner, F.R.4
  • 37
    • 34047191880 scopus 로고    scopus 로고
    • Combined ecological niche modelling and molecular phylogeography revealed the evolutionary history of Hordeum marinum (Poaceae) - niche differentiation, loss of genetic diversity, and speciation in Mediterranean Quaternary refugia
    • Jakob S.S., Ihlow A., Blattner F.R. 2007. Combined ecological niche modelling and molecular phylogeography revealed the evolutionary history of Hordeum marinum (Poaceae) - niche differentiation, loss of genetic diversity, and speciation in Mediterranean Quaternary refugia. Mol. Ecol. 16: 1713-1727.
    • (2007) Mol. Ecol. , vol.16 , pp. 1713-1727
    • Jakob, S.S.1    Ihlow, A.2    Blattner, F.R.3
  • 38
    • 62349092321 scopus 로고    scopus 로고
    • Phylogeographic analyses and paleodistribution modeling indicate Pleistocene in situ survival of Hordeum species (Poaceae) in Southern Patagonia without genetic or spatial restriction
    • Jakob S.S., Martinez-Meyer E., Blattner F.R. 2009. Phylogeographic analyses and paleodistribution modeling indicate Pleistocene in situ survival of Hordeum species (Poaceae) in Southern Patagonia without genetic or spatial restriction. Mol. Biol. Evol. 26: 907-923.
    • (2009) Mol. Biol. Evol. , vol.26 , pp. 907-923
    • Jakob, S.S.1    Martinez-Meyer, E.2    Blattner, F.R.3
  • 39
    • 1942533491 scopus 로고    scopus 로고
    • The considerable genome size variation of Hordeum species (Poaceae) is linked to phylogeny, life form, ecology, and speciation rates
    • Jakob S.S., MeisterA., Blattner F.R. 2004. The considerable genome size variation of Hordeum species (Poaceae) is linked to phylogeny, life form, ecology, and speciation rates. Mol. Biol. Evol. 21: 860-869.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 860-869
    • Jakob S.S. MeisterA.1    Blattner, F.R.2
  • 40
    • 84902954094 scopus 로고    scopus 로고
    • Evolutionary history of wild barley (Hordeum vulgare subsp. Spontaneum) analyzed using multilocus sequence data and paleodistribution modeling
    • Jakob S.S., Rödder D., Engler J.O., Shaaf S., Özkan H., Blattner F.R., Kilian B. 2014. Evolutionary history of wild barley (Hordeum vulgare subsp. spontaneum) analyzed using multilocus sequence data and paleodistribution modeling. Genome Biol. Evol. 6: 685-702.
    • (2014) Genome Biol. Evol. , vol.6 , pp. 685-702
    • Jakob, S.S.1    Rödder, D.2    Engler, J.O.3    Shaaf, S.4    Özkan, H.5    Blattner, F.R.6    Kilian, B.7
  • 41
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Katoh K., Misawa K., Kuma K., Miyata T. 2002. MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30: 3059-3066.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.3    Miyata, T.4
  • 42
    • 45949107473 scopus 로고    scopus 로고
    • Recent developments in the MAFFT multiple sequence alignment program
    • Katoh K., Toh H. 2008. Recent developments in the MAFFT multiple sequence alignment program. Brief. Bioinform. 9: 286-298.
    • (2008) Brief. Bioinform. , vol.9 , pp. 286-298
    • Katoh, K.1    Toh, H.2
  • 43
    • 72549107111 scopus 로고    scopus 로고
    • Evolutionary process of Hordeum brachyantherum 6x and related tetraploid species revealed by nuclear DNA sequences
    • Komatsuda T., Salomon B., Bothmer R. von. 2009. Evolutionary process of Hordeum brachyantherum 6x and related tetraploid species revealed by nuclear DNA sequences. Breed. Sci. 59: 611-616.
    • (2009) Breed. Sci. , vol.59 , pp. 611-616
    • Komatsuda, T.1    Salomon, B.2    Bothmer, R.3
  • 45
    • 33847302458 scopus 로고    scopus 로고
    • Inconsistency of phylogenetic estimates from concatenated data under coalescence
    • Kubatko L.S., Degnan J.H. 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
  • 46
    • 84861380450 scopus 로고    scopus 로고
    • PartitionFinder: Combined selection of partitioning schemesandsubstitution models for phylogenetic analyses
    • Lanfear R., Calcott B., Ho S.Y.W., Guindon S. 2012. PartitionFinder: Combined selection of partitioning schemesandsubstitution models for phylogenetic analyses. Mol. Biol. Evol. 29: 1695-1701.
    • (2012) Mol. Biol. Evol. , vol.29 , pp. 1695-1701
    • Lanfear, R.1    Calcott, B.2    Ho, S.Y.W.3    Guindon, S.4
  • 47
    • 78149256307 scopus 로고    scopus 로고
    • BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis
    • Larget B.R., Kotha S.K., Dewey C.N., Ané C. 2010. BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics 26: 2910-2911.
    • (2010) Bioinformatics , vol.26 , pp. 2910-2911
    • Larget, B.R.1    Kotha, S.K.2    Dewey, C.N.3    Ané, C.4
  • 48
    • 84865266483 scopus 로고    scopus 로고
    • Anchored hybrid enrichment for massively high-throughput phylogenomics
    • Lemmon A.R., Emme S.A., Lemmon E.M. 2012. Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst. Biol. 61: 727-744.
    • (2012) Syst. Biol. , vol.61 , pp. 727-744
    • Lemmon, A.R.1    Emme, S.A.2    Lemmon, E.M.3
  • 49
    • 33646423282 scopus 로고    scopus 로고
    • Allopolyploid origin of Cardamine asarifolia (Brassicaceae): Incongruence between plastid and nuclear ribosomal DNA sequences solved by a single-copy nuclear gene
    • Lihová J., Shimizu K.K., Marhold K. 2006. Allopolyploid origin of Cardamine asarifolia (Brassicaceae): Incongruence between plastid and nuclear ribosomal DNA sequences solved by a single-copy nuclear gene. Mol. Phylogenet. Evol. 39: 759-786.
    • (2006) Mol. Phylogenet. Evol. , vol.39 , pp. 759-786
    • Lihová, J.1    Shimizu, K.K.2    Marhold, K.3
  • 50
    • 85005701859 scopus 로고
    • Giemsa Cbanding in Asiatic taxa of Hordeum section Stenostachys with notes on chromosome morphology
    • Linde-Laursen I., Bothmer R. von, Jacobsen N. 1980. Giemsa Cbanding in Asiatic taxa of Hordeum section Stenostachys with notes on chromosome morphology. Hereditas 93: 235-254.
    • (1980) Hereditas , vol.93 , pp. 235-254
    • Linde-Laursen, I.1    Bothmer, R.2    Jacobsen, N.3
  • 51
    • 0031504952 scopus 로고    scopus 로고
    • Gene trees in species trees
    • MaddisonW.P. 1997. Gene trees in species trees. Syst. Biol. 46: 523-536.
    • (1997) Syst. Biol. , vol.46 , pp. 523-536
    • Maddison, W.P.1
  • 52
    • 84965114132 scopus 로고    scopus 로고
    • From gene trees to a dated allopolyploid network: Insights from the angiosperm genus Viola (Violaceae
    • Marcussen T., Heier L., Brysting A.K., Oxelman B., Jakobsen K.S. 2015. From gene trees to a dated allopolyploid network: Insights from the angiosperm genus Viola (Violaceae). Syst. Biol. 64: 84-101.
    • (2015) Syst. Biol. , vol.64 , pp. 84-101
    • Marcussen, T.1    Heier, L.2    Brysting, A.K.3    Oxelman, B.4    Jakobsen, K.S.5
  • 53
    • 84555186845 scopus 로고    scopus 로고
    • Inferring species networks from gene trees in high-polyploid North American and Hawaiian violets (Viola, Violaceae
    • Marcussen T., Jakobsen K.S., Danihelka J., Ballard H.E., Blaxland K., Brysting A.K., Oxelman B. 2012. Inferring species networks from gene trees in high-polyploid North American and Hawaiian violets (Viola, Violaceae). Syst. Biol. 61: 107-126.
    • (2012) Syst. Biol. , vol.61 , pp. 107-126
    • Marcussen, T.1    Jakobsen, K.S.2    Danihelka, J.3    Ballard, H.E.4    Blaxland, K.5    Brysting, A.K.6    Oxelman, B.7
  • 54
    • 84904402814 scopus 로고    scopus 로고
    • Ancient hybridizations among the ancestral genomes of bread wheat
    • The International Wheat Genome Sequencing Consortium
    • Marcussen T., Sandve S.R., Heier L., SpannaglM., Jakobsen K.S., Pfeifer M., The International Wheat Genome Sequencing Consortium, Wulff B.B.H., Steuernagel B.,Mayer K.F.X., Olsen O.-A. 2014. Ancient hybridizations among the ancestral genomes of bread wheat. Science 345: 1250092-1-1250092-4.
    • (2014) Science , vol.345 , pp. 12500921-12500924
    • Marcussen, T.1    Sandve, S.R.2    Heier, L.3    Spannagl, M.4    Jakobsen, K.S.5    Pfeifer, M.6
  • 57
    • 39449089394 scopus 로고    scopus 로고
    • Parallel tagged sequencing on the 454 platform
    • Meyer M., Stenzel U., Hofreiter M. 2008b. Parallel tagged sequencing on the 454 platform. Nat. Protoc. 3: 267-278.
    • (2008) Nat. Protoc. , vol.3 , pp. 267-278
    • Meyer, M.1    Stenzel, U.2    Hofreiter, M.3
  • 58
    • 1842446349 scopus 로고    scopus 로고
    • Molecular phylogeny of the genus Hordeum using three chloroplast DNA sequences
    • Nishikawa T., Salomon B., Komatsuda T., Bothmer R. von, Kadowaki K. 2002. Molecular phylogeny of the genus Hordeum using three chloroplast DNA sequences. Genome 45: 1157-1166.
    • (2002) Genome , vol.45 , pp. 1157-1166
    • Nishikawa, T.1    Salomon, B.2    Komatsuda, T.3    Bothmer, R.4    Kadowaki, K.5
  • 59
    • 30344473638 scopus 로고    scopus 로고
    • A novel algorithm and webbased tool for comparing two alternative phylogenetic trees
    • Nye T.M.W., Liò P., Gilks W.R. 2006. A novel algorithm and webbased tool for comparing two alternative phylogenetic trees. Bioinformatics 22: 117-119.
    • (2006) Bioinformatics , vol.22 , pp. 117-119
    • Nye, T.M.W.1    Liò, P.2    Gilks, W.R.3
  • 60
    • 39149141072 scopus 로고    scopus 로고
    • AWTY (are we there yet?): A system for graphical exploration of MCMC convergence in Bayesian phylogenetics
    • Nylander J.A.A., Wilgenbusch J.C., Warren D.L., Swofford D.L. 2008. AWTY (are we there yet?): A system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24: 581-583.
    • (2008) Bioinformatics , vol.24 , pp. 581-583
    • Nylander, J.A.A.1    Wilgenbusch, J.C.2    Warren, D.L.3    Swofford, D.L.4
  • 61
    • 84872864542 scopus 로고    scopus 로고
    • Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex
    • O'Neill E.M., Schwartz R., Bullock C.T., Williams J.S., Shaffer H.B., Aguilar-Miguel X., Parra-Olea G., Weisrock D.W. 2013. Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex. Mol. Ecol. 22: 111-129.
    • (2013) Mol. Ecol. , vol.22 , pp. 111-129
    • O'Neill, E.M.1    Schwartz, R.2    Bullock, C.T.3    Williams, J.S.4    Shaffer, H.B.5    Aguilar-Miguel, X.6    Parra-Olea, G.7    Weisrock, D.W.8
  • 63
    • 0023822631 scopus 로고
    • Relationships between gene trees and species trees
    • Pamilo P., Nei M. 1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5: 568-583.
    • (1988) Mol. Biol. Evol. , vol.5 , pp. 568-583
    • Pamilo, P.1    Nei, M.2
  • 64
    • 79960122986 scopus 로고    scopus 로고
    • When is enough, enough in phylogenetics? A case in point from Hordeum (Poaceae
    • Petersen G., Aagesen L., Seberg O., Larsen I.H. 2011. When is enough, enough in phylogenetics? A case in point from Hordeum (Poaceae). Cladistics 27: 428-446.
    • (2011) Cladistics , vol.27 , pp. 428-446
    • Petersen, G.1    Aagesen, L.2    Seberg, O.3    Larsen, I.H.4
  • 65
    • 0037570944 scopus 로고    scopus 로고
    • Phylogenetic analyses of the diploid species of Hordeum (Poaceae) and a revised classification of the genus
    • Petersen G., Seberg O. 2003. Phylogenetic analyses of the diploid species of Hordeum (Poaceae) and a revised classification of the genus. Syst. Bot. 28: 293-306.
    • (2003) Syst. Bot. , vol.28 , pp. 293-306
    • Petersen, G.1    Seberg, O.2
  • 66
    • 8844271005 scopus 로고    scopus 로고
    • On the origin of the tetraploid species Hordeum capense and H. Secalinum (Poaceae
    • Petersen G., Seberg O. 2004. On the origin of the tetraploid species Hordeum capense and H. secalinum (Poaceae). Syst. Bot. 29: 862-873.
    • (2004) Syst. Bot. , vol.29 , pp. 862-873
    • Petersen, G.1    Seberg, O.2
  • 67
    • 48549097447 scopus 로고    scopus 로고
    • Phylogeographic implications of an AFLPphylogeny of theAmerican diploid Hordeum species (Poaceae: Triticeae
    • Pleines T., Blattner F.R. 2008. Phylogeographic implications of an AFLPphylogeny of theAmerican diploid Hordeum species (Poaceae: Triticeae). Taxon 57: 875-881.
    • (2008) Taxon , vol.57 , pp. 875-881
    • Pleines, T.1    Blattner, F.R.2
  • 69
    • 0035527410 scopus 로고    scopus 로고
    • Selecting the best-fit model of nucleotide substitution
    • Posada D., CrandallK.A. 2001. Selecting the best-fit model of nucleotide substitution. Syst. Biol. 50: 580-601.
    • (2001) Syst. Biol. , vol.50 , pp. 580-601
    • Posada, D.1    Crandall, K.A.2
  • 70
    • 79957691064 scopus 로고    scopus 로고
    • Late Cenozoic glaciations in Patagonia and Tierra del Fuego: An updated review
    • Rabassa J., Coronato A., Martínez O. 2011. Late Cenozoic glaciations in Patagonia and Tierra del Fuego: An updated review. Biol. J. Linn. Soc. 103: 316-335.
    • (2011) Biol. J. Linn. Soc. , vol.103 , pp. 316-335
    • Rabassa, J.1    Coronato, A.2    Martínez, O.3
  • 71
    • 77955300661 scopus 로고    scopus 로고
    • Available from: Last accessed June 19, 2015
    • Rambaut A., Drummond A. 2007. Tracer v1.5. Available from: Http://tree.bio.ed.ac.uk/software/tracer/, last accessed June 19, 2015.
    • (2007) Tracer v1.5
    • Rambaut, A.1    Drummond, A.2
  • 73
    • 0028066652 scopus 로고
    • Organelle inheritance in plants
    • Reboud X., Zeyl C. 1994. Organelle inheritance in plants. Heredity 72: 132-140.
    • (1994) Heredity , vol.72 , pp. 132-140
    • Reboud, X.1    Zeyl, C.2
  • 74
    • 0031194327 scopus 로고    scopus 로고
    • Molecular evidence for an extinct parent of the tetraploid species Microseris acuminata and M. Campestris (Asteraceae, Lactuceae
    • Roelofs D., van Velzen J., Kuperus P., Bachmann K. 1997. Molecular evidence for an extinct parent of the tetraploid species Microseris acuminata and M. campestris (Asteraceae, Lactuceae). Mol. Ecol. 6: 641-649.
    • (1997) Mol. Ecol. , vol.6 , pp. 641-649
    • Roelofs, D.1    Van Velzen, J.2    Kuperus, P.3    Bachmann, K.4
  • 76
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou N., Nei M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 77
    • 0031725056 scopus 로고    scopus 로고
    • The ancestry of Hordeum depressum (Poaceae, Triticeae
    • Salomon B., Bothmer R. von. 1998. The ancestry of Hordeum depressum (Poaceae, Triticeae). Nord. J. Bot. 18: 257-265.
    • (1998) Nord. J. Bot. , vol.18 , pp. 257-265
    • Salomon, B.1    Bothmer, R.2
  • 78
    • 0036062110 scopus 로고    scopus 로고
    • Utility of low-copy nuclear gene sequences in plant phylogenetics
    • Sang T. 2002. Utility of low-copy nuclear gene sequences in plant phylogenetics. Crit. Rev. Biochem. Mol. Biol. 37: 121-147.
    • (2002) Crit. Rev. Biochem. Mol. Biol. , vol.37 , pp. 121-147
    • Sang, T.1
  • 80
    • 77953727646 scopus 로고    scopus 로고
    • TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets
    • Schmieder R., Lim Y.W., Rohwer F., Edwards R. 2010. TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets. BMC Bioinformatics 11: 341.
    • (2010) BMC Bioinformatics , vol.11 , pp. 341
    • Schmieder, R.1    Lim, Y.W.2    Rohwer, F.3    Edwards, R.4
  • 81
    • 85006666260 scopus 로고
    • Estimating the dimension of a model
    • Schwarz G. 1978. Estimating the dimension of a model. Ann. Stat. 6: 461-464.
    • (1978) Ann. Stat. , vol.6 , pp. 461-464
    • Schwarz, G.1
  • 82
    • 0346091308 scopus 로고    scopus 로고
    • Use of nuclear genes for phylogeny reconstruction in plants
    • Small R.L., Cronn R.C., Wendel J.F. 2004. Use of nuclear genes for phylogeny reconstruction in plants. Aust. Syst. Bot. 17: 145-170.
    • (2004) Aust. Syst. Bot. , vol.17 , pp. 145-170
    • Small, R.L.1    Cronn, R.C.2    Wendel, J.F.3
  • 83
    • 0033198094 scopus 로고    scopus 로고
    • Polyploidy: Recurrent formation and genome evolution
    • Soltis D.E., Soltis P.S. 1999. Polyploidy: Recurrent formation and genome evolution. Trends Ecol. Evol. 14: 348-352.
    • (1999) Trends Ecol. Evol. , vol.14 , pp. 348-352
    • Soltis, D.E.1    Soltis, P.S.2
  • 86
    • 23644445050 scopus 로고    scopus 로고
    • Ancestry of American polyploid Hordeum species with the I genome inferred from 5S and 18S-25S rDNA
    • Taketa S., Ando H., Takeda K., Ichii M., Bothmer R. von. 2005. Ancestry of American polyploid Hordeum species with the I genome inferred from 5S and 18S-25S rDNA. Ann. Bot. 96: 23-33.
    • (2005) Ann. Bot. , vol.96 , pp. 23-33
    • Taketa, S.1    Ando, H.2    Takeda, K.3    Ichii, M.4    Bothmer, R.5
  • 87
    • 72549088745 scopus 로고    scopus 로고
    • Phylogeny of two tetraploid Hordeum species, H. Secalinum and H. Capense inferred from physical mapping of 5S and 18S-25S rDNA
    • Taketa S., Nakauchi Y., Bothmer R. von. 2009. Phylogeny of two tetraploid Hordeum species, H. secalinum and H. capense inferred from physical mapping of 5S and 18S-25S rDNA. Breed. Sci. 59: 589-594.
    • (2009) Breed. Sci. , vol.59 , pp. 589-594
    • Taketa, S.1    Nakauchi, Y.2    Bothmer, R.3
  • 88
    • 72549084108 scopus 로고    scopus 로고
    • Analysis of DNA sequence polymorphism at the cMWG699 locus reveals phylogenetic relationships and allopolyploidy within Hordeum murinum subspecies
    • Tanno K., Bothmer R. von, Yamane K., Takeda K., Komatsuda T. 2010. Analysis of DNA sequence polymorphism at the cMWG699 locus reveals phylogenetic relationships and allopolyploidy within Hordeum murinum subspecies. Hereditas 147: 34-42.
    • (2010) Hereditas , vol.147 , pp. 34-42
    • Tanno, K.1    Bothmer, R.2    Yamane, K.3    Takeda, K.4    Komatsuda, T.5
  • 89
    • 84870265846 scopus 로고    scopus 로고
    • A physical, genetic and functional sequence assembly of the barley genome
    • The International Barley Genome Sequencing Consortium. 2012. A physical, genetic and functional sequence assembly of the barley genome. Nature 491: 711-716.
    • (2012) Nature , vol.491 , pp. 711-716
  • 90
    • 84862502532 scopus 로고    scopus 로고
    • Five nuclear loci resolve the polyploid history of switchgrass (Panicum virgatum L.) and relatives
    • Triplett J.K., Wang Y., Zhong J., Kellogg E.A. 2012. Five nuclear loci resolve the polyploid history of switchgrass (Panicum virgatum L.) and relatives. PLoS ONE 7: E38702.
    • (2012) PLoS ONE , vol.7 , pp. e38702
    • Triplett, J.K.1    Wang, Y.2    Zhong, J.3    Kellogg, E.A.4
  • 94
    • 84919947905 scopus 로고    scopus 로고
    • Coalescent versus concatenation methods and the placement of Amborella as sister towater lilies
    • Xi Z., Liu L., Rest J.S., Davis C.C. 2014. Coalescent versus concatenation methods and the placement of Amborella as sister towater lilies. Syst. Biol. 63: 919-932.
    • (2014) Syst. Biol. , vol.63 , pp. 919-932
    • Xi, Z.1    Liu, L.2    Rest, J.S.3    Davis, C.C.4
  • 95
    • 84906251283 scopus 로고    scopus 로고
    • Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3
    • Zwickl D.J., Stein J.C., Wing R.A., Ware D., Sanderson M.J. 2014. Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3. Syst. Biol. 63: 645-659.
    • (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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