메뉴 건너뛰기




Volumn 8, Issue 11, 2013, Pages

Phylogenomics and coalescent analyses resolve extant seed plant relationships

Author keywords

[No Author keywords available]

Indexed keywords

CELL NUCLEUS; GENETICS; GENOMICS; GYMNOSPERM; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT GENE; PLANT SEED; PLASTID GENOME; SPECIES DIFFERENCE;

EID: 84894052682     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0080870     Document Type: Article
Times cited : (60)

References (92)
  • 1
    • 0024874652 scopus 로고
    • Elkinsia gen. nov., a late Devonian gymnosperm with cupulate ovules
    • doi:10.1086/337763
    • Rothwell GW, Scheckler SE, Gillespie WH (1989) Elkinsia gen. nov., a late Devonian gymnosperm with cupulate ovules. Bot Gaz 150: 170-189. doi:10.1086/337763.
    • (1989) Bot Gaz , vol.150 , pp. 170-189
    • Rothwell, G.W.1    Scheckler, S.E.2    Gillespie, W.H.3
  • 2
    • 81355160990 scopus 로고    scopus 로고
    • Diversification of land plants: Insights from a family-level phylogenetic analysis
    • doi:10.1186/1471-2148-11-341. PubMed: 22103931
    • Fiz-Palacios O, Schneider H, Heinrichs J, Savolainen V (2011) Diversification of land plants: insights from a family-level phylogenetic analysis. BMC Evol Biol 11: 341. doi:10.1186/1471-2148-11-341. PubMed: 22103931.
    • (2011) BMC Evol Biol , vol.11 , pp. 341
    • Fiz-Palacios, O.1    Schneider, H.2    Heinrichs, J.3    Savolainen, V.4
  • 3
    • 60249093425 scopus 로고    scopus 로고
    • Phylogenetic relationships among seed plants: Persistent questions and the limits of molecular data
    • doi:10.3732/ajb.0800178. PubMed: 21628186
    • Mathews S (2009) Phylogenetic relationships among seed plants: persistent questions and the limits of molecular data. Am J Bot 96: 228-236. doi:10.3732/ajb.0800178. PubMed: 21628186.
    • (2009) Am J Bot , vol.96 , pp. 228-236
    • Mathews, S.1
  • 4
    • 0030052344 scopus 로고    scopus 로고
    • Noncoding sequences from the slowly evolving chloroplast inverted repeat in addition to rbcL data do not support Gnetalean affinities of angiosperms
    • doi:10.1093/oxfordjournals.molbev.a025597. PubMed: 8587503
    • Goremykin V, Bobrova V, Pahnke J, Troitsky A, Antonov A et al. (1996) Noncoding sequences from the slowly evolving chloroplast inverted repeat in addition to rbcL data do not support Gnetalean affinities of angiosperms. Mol Biol Evol 13: 383-396. doi:10.1093/oxfordjournals.molbev.a025597. PubMed: 8587503.
    • (1996) Mol Biol Evol , vol.13 , pp. 383-396
    • Goremykin, V.1    Bobrova, V.2    Pahnke, J.3    Troitsky, A.4    Antonov, A.5
  • 5
    • 0031012107 scopus 로고    scopus 로고
    • Molecular phylogeny of extant gymnosperms and seed plant evolution: Analysis of nuclear 18S rRNA sequences
    • doi:10.1093/oxfordjournals.molbev.a025702. PubMed: 9000754
    • Chaw SM, Zharkikh A, Sung HM, Lau TC, Li WH (1997) Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences. Mol Biol Evol 14: 56-68. doi:10.1093/oxfordjournals.molbev.a025702. PubMed: 9000754.
    • (1997) Mol Biol Evol , vol.14 , pp. 56-68
    • Chaw, S.M.1    Zharkikh, A.2    Sung, H.M.3    Lau, T.C.4    Li, W.H.5
  • 6
    • 0032853708 scopus 로고    scopus 로고
    • Molecular data from the chloroplast rpoC1 gene suggest deep and distinct dichotomy of contemporary spermatophytes into two monophyla: Gymnosperms (including Gnetales) and angiosperms
    • doi:10.1007/PL00006553. PubMed: 10473771
    • Samigullin TK, Martin WF, Troitsky AV, Antonov AS (1999) Molecular data from the chloroplast rpoC1 gene suggest deep and distinct dichotomy of contemporary spermatophytes into two monophyla: gymnosperms (including Gnetales) and angiosperms. J Mol Evol 49: 310-315. doi:10.1007/PL00006553. PubMed: 10473771.
    • (1999) J Mol Evol , vol.49 , pp. 310-315
    • Samigullin, T.K.1    Martin, W.F.2    Troitsky, A.V.3    Antonov, A.S.4
  • 7
    • 0034636023 scopus 로고    scopus 로고
    • Phylogeny of seed plants based on all three genomic compartments: Extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers
    • doi:10.1073/pnas.97.8.4092. PubMed: 10760278
    • Bowe LM, Coat G, dePamphilis CW (2000) Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers. Proc Natl Acad Sci U S A 97: 4092-4097. doi:10.1073/pnas.97.8.4092. PubMed: 10760278.
    • (2000) Proc Natl Acad Sci U S A , vol.97 , pp. 4092-4097
    • Bowe, L.M.1    Coat, G.2    DePamphilis, C.W.3
  • 8
    • 0034636037 scopus 로고    scopus 로고
    • Seed plant phylogeny inferred from all three plant genomes: Monophyly of extant gymnosperms and origin of Gnetales from conifers
    • doi:10.1073/pnas.97.8.4086. PubMed: 10760277
    • Chaw SM, Parkinson CL, Cheng YC, Vincent TM, Palmer JD (2000) Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers. Proc Natl Acad Sci U S A 97: 4086-4091. doi:10.1073/pnas.97.8.4086. PubMed: 10760277.
    • (2000) Proc Natl Acad Sci U S A , vol.97 , pp. 4086-4091
    • Chaw, S.M.1    Parkinson, C.L.2    Cheng, Y.C.3    Vincent, T.M.4    Palmer, J.D.5
  • 9
    • 0033638953 scopus 로고    scopus 로고
    • Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants
    • doi:10.1093/oxfordjournals.molbev.a026290. PubMed: 11110905
    • Nickrent DL, Parkinson CL, Palmer JD, Duff RJ (2000) Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants. Mol Biol Evol 17: 1885-1895. doi:10.1093/oxfordjournals.molbev.a026290. PubMed: 11110905.
    • (2000) Mol Biol Evol , vol.17 , pp. 1885-1895
    • Nickrent, D.L.1    Parkinson, C.L.2    Palmer, J.D.3    Duff, R.J.4
  • 10
    • 0035197346 scopus 로고    scopus 로고
    • The evolutionary split of Pinaceae from other conifers: Evidence from an intron loss and a multigene phylogeny
    • doi:10.1006/mpev.2001.1004. PubMed: 11697913
    • Gugerli F, Sperisen C, Büchler U, Brunner L, Brodbeck S et al. (2001) The evolutionary split of Pinaceae from other conifers: evidence from an intron loss and a multigene phylogeny. Mol Phylogenet Evol 21: 167-175. doi:10.1006/mpev.2001.1004. PubMed: 11697913.
    • (2001) Mol Phylogenet Evol , vol.21 , pp. 167-175
    • Gugerli, F.1    Sperisen, C.2    Büchler, U.3    Brunner, L.4    Brodbeck, S.5
  • 11
    • 0036800892 scopus 로고    scopus 로고
    • Phylogeny of seed plants based on evidence from eight genes
    • doi:10.3732/ajb.89.10.1670. PubMed: 21665594
    • Soltis DE, Soltis PS, Zanis MJ (2002) Phylogeny of seed plants based on evidence from eight genes. Am J Bot 89: 1670-1681. doi:10.3732/ajb.89.10.1670. PubMed: 21665594.
    • (2002) Am J Bot , vol.89 , pp. 1670-1681
    • Soltis, D.E.1    Soltis, P.S.2    Zanis, M.J.3
  • 12
    • 76749130170 scopus 로고    scopus 로고
    • A duplicate gene rooting of seed plants and the phylogenetic position of flowering plants
    • doi:10.1098/rstb.2009.0233. PubMed: 20047866
    • Mathews S, Clements MD, Beilstein MA (2010) A duplicate gene rooting of seed plants and the phylogenetic position of flowering plants. Philos Trans R Soc Lond B Biol Sci 365: 383-395. doi:10.1098/rstb.2009.0233. PubMed: 20047866.
    • (2010) Philos Trans R Soc Lond B Biol Sci , vol.365 , pp. 383-395
    • Mathews, S.1    Clements, M.D.2    Beilstein, M.A.3
  • 13
    • 0000863074 scopus 로고
    • Phylogenetic analysis of seed plants and the origin of angiosperms
    • doi: 10.2307/2399221
    • Crane PR (1985) Phylogenetic analysis of seed plants and the origin of angiosperms. Ann Missouri Bot Gard 72: 716-793. doi: 10.2307/2399221.
    • (1985) Ann Missouri Bot Gard , vol.72 , pp. 716-793
    • Crane, P.R.1
  • 14
    • 0001234321 scopus 로고
    • Seed plant phylogeny and the origin of angiosperms: An experimental cladistic approach
    • doi:10.1007/BF02861082
    • Doyle JA, Donoghue MJ (1986) Seed plant phylogeny and the origin of angiosperms: an experimental cladistic approach. Bot Rev 52: 321-431. doi:10.1007/BF02861082.
    • (1986) Bot Rev , vol.52 , pp. 321-431
    • Doyle, J.A.1    Donoghue, M.J.2
  • 15
    • 84876525951 scopus 로고    scopus 로고
    • Chloroplast phylogenomics indicates that Ginkgo biloba is sister to cycads
    • doi:10.1093/gbe/evt001. PubMed: 23315384
    • Wu CS, Chaw SM, Huang YY (2013) Chloroplast phylogenomics indicates that Ginkgo biloba is sister to cycads. Genome Biol Evol 5: 243-254. doi:10.1093/gbe/evt001. PubMed: 23315384.
    • (2013) Genome Biol Evol , vol.5 , pp. 243-254
    • Wu, C.S.1    Chaw, S.M.2    Huang, Y.Y.3
  • 16
    • 10644238478 scopus 로고    scopus 로고
    • Phylogenetic signal in nucleotide data from seed plants: Implications for resolving the seed plant tree of life
    • doi:10.3732/ajb.91.10.1599. PubMed: 21652311
    • Burleigh JG, Mathews S (2004) Phylogenetic signal in nucleotide data from seed plants: implications for resolving the seed plant tree of life. Am J Bot 91: 1599-1613. doi:10.3732/ajb.91.10.1599. PubMed: 21652311.
    • (2004) Am J Bot , vol.91 , pp. 1599-1613
    • Burleigh, J.G.1    Mathews, S.2
  • 17
    • 33745120503 scopus 로고    scopus 로고
    • Seed plant phylogeny: Gnetophytes are derived conifers and a sister group to Pinaceae
    • doi:10.1016/j.ympev.2006.03.006. PubMed: 16621615
    • Hajibabaei M, Xia JN, Drouin G (2006) Seed plant phylogeny: gnetophytes are derived conifers and a sister group to Pinaceae. Mol Phylogenet Evol 40: 208-217. doi:10.1016/j.ympev.2006.03.006. PubMed: 16621615.
    • (2006) Mol Phylogenet Evol , vol.40 , pp. 208-217
    • Hajibabaei, M.1    Xia, J.N.2    Drouin, G.3
  • 18
    • 34249807028 scopus 로고    scopus 로고
    • A nonflowering land plant phylogeny inferred from nucleotide sequences of seven chloroplast, mitochondrial, and nuclear genes
    • doi:10.1086/513474
    • Qiu YL, Li LB, Wang B, Chen ZD, Dombrovska O et al. (2007) A nonflowering land plant phylogeny inferred from nucleotide sequences of seven chloroplast, mitochondrial, and nuclear genes. Int J Plant Sci 168: 691-708. doi:10.1086/513474.
    • (2007) Int J Plant Sci , vol.168 , pp. 691-708
    • Qiu, Y.L.1    Li, L.B.2    Wang, B.3    Chen, Z.D.4    Dombrovska, O.5
  • 19
    • 78650511270 scopus 로고    scopus 로고
    • Multigene phylogeny of the green lineage reveals the origin and diversification of land plants
    • doi:10.1016/j.cub.2010.11.035. PubMed: 21145743
    • Finet C, Timme RE, Delwiche CF, Marlétaz F (2010) Multigene phylogeny of the green lineage reveals the origin and diversification of land plants. Curr Biol 20: 2217-2222. doi:10.1016/j.cub.2010.11.035. PubMed: 21145743.
    • (2010) Curr Biol , vol.20 , pp. 2217-2222
    • Finet, C.1    Timme, R.E.2    Delwiche, C.F.3    Marlétaz, F.4
  • 20
    • 77954143435 scopus 로고    scopus 로고
    • Lineage-specific group II intron gains and losses of the mitochondrial rps3 gene in gymnosperms
    • doi:10.1016/j.plaphy.2010.05.003. PubMed: 20605476
    • Regina TMR, Quagliariello C (2010) Lineage-specific group II intron gains and losses of the mitochondrial rps3 gene in gymnosperms. Plant Physiol Biochem 48: 646-654. doi:10.1016/j.plaphy.2010.05.003. PubMed: 20605476.
    • (2010) Plant Physiol Biochem , vol.48 , pp. 646-654
    • Regina, T.M.R.1    Quagliariello, C.2
  • 21
    • 78649362791 scopus 로고    scopus 로고
    • The position of gnetales among seed plants: Overcoming pitfalls of chloroplast phylogenomics
    • doi:10.1093/molbev/msq170. PubMed: 20601411
    • Zhong B, Yonezawa T, Zhong Y, Hasegawa M (2010) The position of gnetales among seed plants: overcoming pitfalls of chloroplast phylogenomics. Mol Biol Evol 27: 2855-2863. doi:10.1093/molbev/msq170. PubMed: 20601411.
    • (2010) Mol Biol Evol , vol.27 , pp. 2855-2863
    • Zhong, B.1    Yonezawa, T.2    Zhong, Y.3    Hasegawa, M.4
  • 22
    • 79955104313 scopus 로고    scopus 로고
    • Origin of land plants: Do conjugating green algae hold the key?
    • doi:10.1186/1471-2148-11-104. PubMed: 21501468
    • Wodniok S, Brinkmann H, Glöckner G, Heidel AJ, Philippe H et al. (2011) Origin of land plants: do conjugating green algae hold the key? BMC Evol Biol 11: 104. doi:10.1186/1471-2148-11-104. PubMed: 21501468.
    • (2011) BMC Evol Biol , vol.11 , pp. 104
    • Wodniok, S.1    Brinkmann, H.2    Glöckner, G.3    Heidel, A.J.4    Philippe, H.5
  • 23
    • 84855848337 scopus 로고    scopus 로고
    • Loss of different inverted repeat copies from the chloroplast genomes of Pinaceae and cupressophytes and influence of heterotachy on the evaluation of gymnosperm phylogeny
    • doi: 10.1093/gbe/evr095. PubMed: 21933779
    • Wu CS, Wang YN, Hsu CY, Lin CP, Chaw SM (2011) Loss of different inverted repeat copies from the chloroplast genomes of Pinaceae and cupressophytes and influence of heterotachy on the evaluation of gymnosperm phylogeny. Genome Biol Evol 3: 1284-1295. doi: 10.1093/gbe/evr095. PubMed: 21933779.
    • (2011) Genome Biol Evol , vol.3 , pp. 1284-1295
    • Wu, C.S.1    Wang, Y.N.2    Hsu, C.Y.3    Lin, C.P.4    Chaw, S.M.5
  • 24
    • 84859115343 scopus 로고    scopus 로고
    • Systematic error in seed plant phylogenomics
    • doi:10.1093/gbe/evr105. PubMed: 22016337
    • Zhong B, Deusch O, Goremykin VV, Penny D, Biggs PJ et al. (2011) Systematic error in seed plant phylogenomics. Genome Biol Evol 3: 1340-1348. doi:10.1093/gbe/evr105. PubMed: 22016337.
    • (2011) Genome Biol Evol , vol.3 , pp. 1340-1348
    • Zhong, B.1    Deusch, O.2    Goremykin, V.V.3    Penny, D.4    Biggs, P.J.5
  • 25
    • 70649103857 scopus 로고    scopus 로고
    • Fast evolution of the retroprocessed mitochondrial rps3 gene in Conifer II and further evidence for the phylogeny of gymnosperms
    • doi: 10.1016/j.ympev.2009.09.011. PubMed: 19761858
    • Ran JH, Gao H, Wang XQ (2010) Fast evolution of the retroprocessed mitochondrial rps3 gene in Conifer II and further evidence for the phylogeny of gymnosperms. Mol Phylogenet Evol 54: 136-149. doi: 10.1016/j.ympev.2009.09.011. PubMed: 19761858.
    • (2010) Mol Phylogenet Evol , vol.54 , pp. 136-149
    • Ran, J.H.1    Gao, H.2    Wang, X.Q.3
  • 26
    • 0033604548 scopus 로고    scopus 로고
    • The earliest angiosperms: Evidence from mitochondrial, plastid and nuclear genomes
    • doi:10.1038/46536. PubMed: 10586879
    • Qiu YL, Lee JH, Bernasconi-Quadroni F, Soltis DE, Soltis PS et al. (1999) The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes. Nature 402: 404-407. doi:10.1038/46536. PubMed: 10586879.
    • (1999) Nature , vol.402 , pp. 404-407
    • Qiu, Y.L.1    Lee, J.H.2    Bernasconi-Quadroni, F.3    Soltis, D.E.4    Soltis, P.S.5
  • 27
    • 0033677575 scopus 로고    scopus 로고
    • Phylogeny of basal angiosperms: Analyses of five genes from three genomes
    • doi:10.1086/317584
    • Qiu YL, Lee J, Bernasconi-Quadroni F, Soltis DE, Soltis PS et al. (2000) Phylogeny of basal angiosperms: analyses of five genes from three genomes. Int J Plant Sci 161: S3-S27. doi:10.1086/317584.
    • (2000) Int J Plant Sci , vol.161
    • Qiu, Y.L.1    Lee, J.2    Bernasconi-Quadroni, F.3    Soltis, D.E.4    Soltis, P.S.5
  • 28
    • 33750020704 scopus 로고    scopus 로고
    • Reconstructing the basal angiosperm phylogeny: Evaluating information content of mitochondrial genes
    • doi: 10.2307/25065680
    • Qiu YL, Li LB, Hendry TA, Li RQ, Taylor DW et al. (2006) Reconstructing the basal angiosperm phylogeny: evaluating information content of mitochondrial genes. Taxon 55: 837-856. doi: 10.2307/25065680.
    • (2006) Taxon , vol.55 , pp. 837-856
    • Qiu, Y.L.1    Li, L.B.2    Hendry, T.A.3    Li, R.Q.4    Taylor, D.W.5
  • 29
    • 33750303564 scopus 로고    scopus 로고
    • The deepest divergences in land plants inferred from phylogenomic evidence
    • doi:10.1073/pnas.0603335103. PubMed: 17030812
    • Qiu YL, Li LB, Wang B, Chen ZD, Knoop V et al. (2006) The deepest divergences in land plants inferred from phylogenomic evidence. Proc Natl Acad Sci U S A 103: 15511-15516. doi:10.1073/pnas.0603335103. PubMed: 17030812.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 15511-15516
    • Qiu, Y.L.1    Li, L.B.2    Wang, B.3    Chen, Z.D.4    Knoop, V.5
  • 30
    • 34548108492 scopus 로고    scopus 로고
    • Chloroplast genome (cpDNA) of Cycas taitungensis and 56 cp protein-coding genes of Gnetum parvifolium: Insights into cpDNA evolution and phylogeny of extant seed plants
    • doi:10.1093/molbev/msm059. PubMed: 17383970
    • Wu CS, Wang YN, Liu SM, Chaw SM (2007) Chloroplast genome (cpDNA) of Cycas taitungensis and 56 cp protein-coding genes of Gnetum parvifolium: Insights into cpDNA evolution and phylogeny of extant seed plants. Mol Biol Evol 24: 1366-1379. doi:10.1093/molbev/msm059. PubMed: 17383970.
    • (2007) Mol Biol Evol , vol.24 , pp. 1366-1379
    • Wu, C.S.1    Wang, Y.N.2    Liu, S.M.3    Chaw, S.M.4
  • 31
    • 0036177790 scopus 로고    scopus 로고
    • Seed plant relationships and the systematic position of Gnetales based on nuclear and chloroplast DNA: Conflicting data, rooting problems, and the monophyly of conifers
    • doi:10.1086/338321
    • Rydin C, Kallersjo M, Friist EM (2002) Seed plant relationships and the systematic position of Gnetales based on nuclear and chloroplast DNA: conflicting data, rooting problems, and the monophyly of conifers. Int J Plant Sci 163: 197-214. doi:10.1086/338321.
    • (2002) Int J Plant Sci , vol.163 , pp. 197-214
    • Rydin, C.1    Kallersjo, M.2    Friist, E.M.3
  • 32
    • 33847243366 scopus 로고    scopus 로고
    • Assessing among-locus variation in the inference of seed plant phylogeny
    • doi: 10.1086/509586
    • Burleigh JG, Mathews S (2007) Assessing among-locus variation in the inference of seed plant phylogeny. Int J Plant Sci 168: 111-124. doi: 10.1086/509586.
    • (2007) Int J Plant Sci , vol.168 , pp. 111-124
    • Burleigh, J.G.1    Mathews, S.2
  • 33
    • 47649087623 scopus 로고    scopus 로고
    • Inference of higher-order conifer relationships from a multi-locus plastid data set
    • doi:10.1139/B08-062
    • Rai HS, Reeves PA, Peakall R, Olmstead RG, Graham SW (2008) Inference of higher-order conifer relationships from a multi-locus plastid data set. Botany 86: 658-669. doi:10.1139/B08-062.
    • (2008) Botany , vol.86 , pp. 658-669
    • Rai, H.S.1    Reeves, P.A.2    Peakall, R.3    Olmstead, R.G.4    Graham, S.W.5
  • 34
    • 66749144092 scopus 로고    scopus 로고
    • The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data
    • doi:10.1371/journal.pone.0005764. PubMed: 19503618
    • de la Torre-Bárcena JE, Kolokotronis SO, Lee EK, Stevenson DW, Brenner ED et al. (2009) The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data. PLOS ONE 4: e5764. doi:10.1371/journal.pone.0005764. PubMed: 19503618.
    • (2009) PLOS ONE , vol.4
    • De La Torre-Bárcena, J.E.1    Kolokotronis, S.O.2    Lee, E.K.3    Stevenson, D.W.4    Brenner, E.D.5
  • 35
    • 60249089451 scopus 로고    scopus 로고
    • Different gymnosperm outgroups have (mostly) congruent signal regarding the root of flowering plant phylogeny
    • doi:10.3732/ajb.0800320. PubMed: 21628185
    • Graham SW, Iles WJD (2009) Different gymnosperm outgroups have (mostly) congruent signal regarding the root of flowering plant phylogeny. Am J Bot 96: 216-227. doi:10.3732/ajb.0800320. PubMed: 21628185.
    • (2009) Am J Bot , vol.96 , pp. 216-227
    • Graham, S.W.1    Iles, W.J.D.2
  • 36
    • 77958474295 scopus 로고    scopus 로고
    • Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution
    • doi:10.1093/gbe/evq012. PubMed: 20624728
    • Cibrián-Jaramillo A, De la Torre-Bárcena JE, Lee EK, Katari MS, Little DP et al. (2010) Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution. Genome Biol Evol 2: 225-239. doi:10.1093/gbe/evq012. PubMed: 20624728.
    • (2010) Genome Biol Evol , vol.2 , pp. 225-239
    • Cibrián-Jaramillo, A.1    De La Torre-Bárcena, J.E.2    Lee, E.K.3    Katari, M.S.4    Little, D.P.5
  • 38
    • 0029751363 scopus 로고    scopus 로고
    • Combining data in phylogenetic analysis
    • doi: 10.1016/0169-5347(96)10006-9. PubMed: 21237790
    • Huelsenbeck JP, Bull JJ, Cunningham CW (1996) Combining data in phylogenetic analysis. Trends Ecol Evol 11: 152-158. doi: 10.1016/0169-5347(96) 10006-9. PubMed: 21237790.
    • (1996) Trends Ecol Evol , vol.11 , pp. 152-158
    • Huelsenbeck, J.P.1    Bull, J.J.2    Cunningham, C.W.3
  • 39
    • 25844516325 scopus 로고    scopus 로고
    • Phylogenetic MCMC algorithms are misleading on mixtures of trees
    • doi:10.1126/science.1115493. PubMed: 16195459
    • Mossel E, Vigoda E (2005) Phylogenetic MCMC algorithms are misleading on mixtures of trees. Science 309: 2207-2209. doi:10.1126/science.1115493. PubMed: 16195459.
    • (2005) Science , vol.309 , pp. 2207-2209
    • Mossel, E.1    Vigoda, E.2
  • 40
    • 33646928341 scopus 로고    scopus 로고
    • Discordance of species trees with their most likely gene trees
    • doi:10.1371/journal.pgen.0020068. PubMed: 16733550
    • Degnan JH, Rosenberg NA (2006) Discordance of species trees with their most likely gene trees. PLoS Genet 2: e68. doi:10.1371/journal.pgen.0020068. PubMed: 16733550.
    • (2006) PLoS Genet , vol.2
    • Degnan, J.H.1    Rosenberg, N.A.2
  • 41
    • 33847302458 scopus 로고    scopus 로고
    • Inconsistency of phylogenetic estimates from concatenated data under coalescence
    • doi:10.1080/10635150601146041. PubMed: 17366134
    • Kubatko LS, Degnan JH (2007) Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst Biol 56: 17-24. doi:10.1080/ 10635150601146041. PubMed: 17366134.
    • (2007) Syst Biol , vol.56 , pp. 17-24
    • Kubatko, L.S.1    Degnan, J.H.2
  • 42
    • 47749087905 scopus 로고    scopus 로고
    • Discordance of species trees with their most likely gene trees: The case of five taxa
    • doi: 10.1080/10635150801905535. PubMed: 18300026
    • Rosenberg NA, Tao R (2008) Discordance of species trees with their most likely gene trees: the case of five taxa. Syst Biol 57: 131-140. doi: 10.1080/10635150801905535. PubMed: 18300026.
    • (2008) Syst Biol , vol.57 , pp. 131-140
    • Rosenberg, N.A.1    Tao, R.2
  • 43
    • 70349417912 scopus 로고    scopus 로고
    • Phylogenetic analysis in the anomaly zone
    • doi:10.1093/sysbio/syp034. PubMed: 20525599
    • Liu L, Edwards SV (2009) Phylogenetic analysis in the anomaly zone. Syst Biol 58: 452-460. doi:10.1093/sysbio/syp034. PubMed: 20525599.
    • (2009) Syst Biol , vol.58 , pp. 452-460
    • Liu, L.1    Edwards, S.V.2
  • 44
    • 47749093183 scopus 로고    scopus 로고
    • Estimating species trees using multiple-allele DNA sequence data
    • doi:10.1111/j.1558-5646.2008.00414.x. PubMed: 18462214
    • Liu L, Pearl DK, Brumfield RT, Edwards SV (2008) Estimating species trees using multiple-allele DNA sequence data. Evolution 62: 2080-2091. doi:10.1111/j.1558-5646.2008.00414.x. PubMed: 18462214.
    • (2008) Evolution , vol.62 , pp. 2080-2091
    • Liu, L.1    Pearl, D.K.2    Brumfield, R.T.3    Edwards, S.V.4
  • 45
    • 65649131928 scopus 로고    scopus 로고
    • Gene tree discordance, phylogenetic inference and the multispecies coalescent
    • doi:10.1016/j.tree.2009.01.009. PubMed: 19307040
    • Degnan JH, Rosenberg NA (2009) Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol 24: 332-340. doi:10.1016/j.tree.2009.01.009. PubMed: 19307040.
    • (2009) Trends Ecol Evol , vol.24 , pp. 332-340
    • Degnan, J.H.1    Rosenberg, N.A.2
  • 46
    • 70349425459 scopus 로고    scopus 로고
    • Estimating species phylogenies using coalescence times among sequences
    • doi:10.1093/sysbio/syp031. PubMed: 20525601
    • Liu L, Yu L, Pearl DK, Edwards SV (2009) Estimating species phylogenies using coalescence times among sequences. Syst Biol 58: 468-477. doi:10.1093/sysbio/syp031. PubMed: 20525601.
    • (2009) Syst Biol , vol.58 , pp. 468-477
    • Liu, L.1    Yu, L.2    Pearl, D.K.3    Edwards, S.V.4
  • 47
    • 77957686501 scopus 로고    scopus 로고
    • A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
    • doi:10.1186/1471-2148-10-302. PubMed: 20937096
    • Liu L, Yu L, Edwards SV (2010) A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol Biol 10: 302. doi:10.1186/1471-2148-10-302. PubMed: 20937096.
    • (2010) BMC Evol Biol , vol.10 , pp. 302
    • Liu, L.1    Yu, L.2    Edwards, S.V.3
  • 48
    • 84866289853 scopus 로고    scopus 로고
    • Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
    • doi:10.1073/pnas.1211733109. PubMed: 22930817
    • Song S, Liu L, Edwards SV, Wu S (2012) Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proc Natl Acad Sci U S A 109: 14942-14947. doi:10.1073/pnas.1211733109. PubMed: 22930817.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 14942-14947
    • Song, S.1    Liu, L.2    Edwards, S.V.3    Wu, S.4
  • 49
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • doi:10.1093/nar/30.7.1575. PubMed: 11917018
    • Enright AJ, van Dongen S, Ouzounis CA (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30: 1575-1584. doi:10.1093/nar/30.7.1575. PubMed: 11917018.
    • (2002) Nucleic Acids Res , vol.30 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.2    Ouzounis, C.A.3
  • 51
    • 79955630390 scopus 로고    scopus 로고
    • Ancestral polyploidy in seed plants and angiosperms
    • doi:10.1038/nature09916. PubMed: 21478875
    • Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L et al. (2011) Ancestral polyploidy in seed plants and angiosperms. Nature 473: 97-100. doi:10.1038/nature09916. PubMed: 21478875.
    • (2011) Nature , vol.473 , pp. 97-100
    • Jiao, Y.1    Wickett, N.J.2    Ayyampalayam, S.3    Chanderbali, A.S.4    Landherr, L.5
  • 52
    • 79956309501 scopus 로고    scopus 로고
    • The Selaginella genome identifies genetic changes associated with the evolution of vascular plants
    • doi: 10.1126/science.1203810. PubMed: 21551031
    • Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M et al. (2011) The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science 332: 960-963. doi: 10.1126/science.1203810. PubMed: 21551031.
    • (2011) Science , vol.332 , pp. 960-963
    • Banks, J.A.1    Nishiyama, T.2    Hasebe, M.3    Bowman, J.L.4    Gribskov, M.5
  • 53
    • 0000596691 scopus 로고
    • Interspecific chloroplast recombination in a Nicotiana somatic hybrid
    • doi:10.1073/pnas.82.20.6960. PubMed: 16593619
    • Medgyesy P, Fejes E, Maliga P (1985) Interspecific chloroplast recombination in a Nicotiana somatic hybrid. Proc Natl Acad Sci U S A 82: 6960-6964. doi:10.1073/pnas.82.20.6960. PubMed: 16593619.
    • (1985) Proc Natl Acad Sci U S A , vol.82 , pp. 6960-6964
    • Medgyesy, P.1    Fejes, E.2    Maliga, P.3
  • 54
    • 0024110615 scopus 로고
    • Intramolecular recombination of chloroplast genome mediated by short direct-repeat sequences in wheat species
    • doi:10.1073/pnas.85.22.8573. PubMed: 3186748
    • Ogihara Y, Terachi T, Sasakuma T (1988) Intramolecular recombination of chloroplast genome mediated by short direct-repeat sequences in wheat species. Proc Natl Acad Sci U S A 85: 8573-8577. doi:10.1073/pnas.85.22.8573. PubMed: 3186748.
    • (1988) Proc Natl Acad Sci U S A , vol.85 , pp. 8573-8577
    • Ogihara, Y.1    Terachi, T.2    Sasakuma, T.3
  • 55
    • 0029159580 scopus 로고
    • Chloroplast DNA variation in Populus. III. Novel chloroplast DNA variants in natural Populus x canadensis hybrids
    • PubMed: 24173921
    • Rajora OP, Dancik BP (1995) Chloroplast DNA variation in Populus. III. Novel chloroplast DNA variants in natural Populus x canadensis hybrids. Theor Appl Genet 90: 331-334. PubMed: 24173921.
    • (1995) Theor Appl Genet , vol.90 , pp. 331-334
    • Rajora, O.P.1    Dancik, B.P.2
  • 56
    • 8844267682 scopus 로고    scopus 로고
    • Recombination, heteroplasmy, haplotype polymorphism, and paralogy in plastid genes: Implications for plant molecular systematics
    • doi: 10.1600/0363644042451008
    • Wolfe AD, Randle CP (2004) Recombination, heteroplasmy, haplotype polymorphism, and paralogy in plastid genes: Implications for plant molecular systematics. Syst Bot 29: 1011-1020. doi: 10.1600/0363644042451008.
    • (2004) Syst Bot , vol.29 , pp. 1011-1020
    • Wolfe, A.D.1    Randle, C.P.2
  • 57
    • 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
    • doi:10.1093/molbev/msl018. PubMed: 16754643
    • Jakob SS, Blattner FR (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. doi:10.1093/molbev/msl018. PubMed: 16754643.
    • (2006) Mol Biol Evol , vol.23 , pp. 1602-1612
    • Jakob, S.S.1    Blattner, F.R.2
  • 58
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • doi:10.1093/bioinformatics/btl446. PubMed: 16928733
    • Stamatakis A (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690. doi:10.1093/bioinformatics/btl446. PubMed: 16928733.
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 59
    • 50949129519 scopus 로고    scopus 로고
    • Calculating bootstrap probabilities of phylogeny using multilocus sequence data
    • doi:10.1093/molbev/msn043. PubMed: 18281270
    • Seo TK (2008) Calculating bootstrap probabilities of phylogeny using multilocus sequence data. Mol Biol Evol 25: 960-971. doi:10.1093/molbev/msn043. PubMed: 18281270.
    • (2008) Mol Biol Evol , vol.25 , pp. 960-971
    • Seo, T.K.1
  • 60
    • 0036623258 scopus 로고    scopus 로고
    • An approximately unbiased test of phylogenetic tree selection
    • doi: 10.1080/10635150290069913. PubMed: 12079646
    • Shimodaira H (2002) An approximately unbiased test of phylogenetic tree selection. Syst Biol 51: 492-508. doi: 10.1080/10635150290069913. PubMed: 12079646.
    • (2002) Syst Biol , vol.51 , pp. 492-508
    • Shimodaira, H.1
  • 61
    • 0023498406 scopus 로고
    • Earliest phylogenetic branchings: Comparing rRNA-based evolutionary trees inferred with various techniques
    • doi:10.1101/SQB.1987.052.01.090. PubMed: 3454291
    • Olsen GJ (1987) Earliest phylogenetic branchings: comparing rRNA-based evolutionary trees inferred with various techniques. Cold Spring Harb Symp Quant Biol 52: 825-837. doi:10.1101/SQB.1987.052.01.090. PubMed: 3454291.
    • (1987) Cold Spring Harb Symp Quant Biol , vol.52 , pp. 825-837
    • Olsen, G.J.1
  • 62
    • 78649982886 scopus 로고    scopus 로고
    • Automated removal of noisy data in phylogenomic analyses
    • doi:10.1007/s00239-010-9398-z. PubMed: 20976444
    • Goremykin VV, Nikiforova SV, Bininda-Emonds OR (2010) Automated removal of noisy data in phylogenomic analyses. J Mol Evol 71: 319-331. doi:10.1007/s00239-010-9398-z. PubMed: 20976444.
    • (2010) J Mol Evol , vol.71 , pp. 319-331
    • Goremykin, V.V.1    Nikiforova, S.V.2    Bininda-Emonds, O.R.3
  • 63
    • 0033015732 scopus 로고    scopus 로고
    • Archaea sister group of bacteria? Indications from tree reconstruction artifacts in ancient phylogenies
    • doi:10.1093/oxfordjournals.molbev.a026166. PubMed: 10368959
    • Brinkmann H, Philippe H (1999) Archaea sister group of bacteria? Indications from tree reconstruction artifacts in ancient phylogenies. Mol Biol Evol 16: 817-825. doi:10.1093/oxfordjournals.molbev.a026166. PubMed: 10368959.
    • (1999) Mol Biol Evol , vol.16 , pp. 817-825
    • Brinkmann, H.1    Philippe, H.2
  • 64
    • 0033582323 scopus 로고    scopus 로고
    • Microsporidia are related to Fungi: Evidence from the largest subunit of RNA polymerase II and other proteins
    • doi:10.1073/pnas.96.2.580. PubMed: 9892676
    • Hirt RP, Logsdon JM, Healy B, Dorey MW, Doolittle WF et al. (1999) Microsporidia are related to Fungi: evidence from the largest subunit of RNA polymerase II and other proteins. Proc Natl Acad Sci U S A 96: 580-585. doi:10.1073/pnas.96.2.580. PubMed: 9892676.
    • (1999) Proc Natl Acad Sci U S A , vol.96 , pp. 580-585
    • Hirt, R.P.1    Logsdon, J.M.2    Healy, B.3    Dorey, M.W.4    Doolittle, W.F.5
  • 65
    • 0034702256 scopus 로고    scopus 로고
    • Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions
    • doi:10.1098/rspb.2000.1130. PubMed: 10902687
    • Philippe H, Lopez P, Brinkmann H, Budin K, Germot A et al. (2000) Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions. Proc Biol Sci 267: 1213-1221. doi:10.1098/rspb.2000.1130. PubMed: 10902687.
    • (2000) Proc Biol Sci , vol.267 , pp. 1213-1221
    • Philippe, H.1    Lopez, P.2    Brinkmann, H.3    Budin, K.4    Germot, A.5
  • 66
    • 0036593395 scopus 로고    scopus 로고
    • Ancient phylogenetic relationships
    • doi:10.1006/tpbi.2002.1593. PubMed: 12167360
    • Gribaldo S, Philippe H (2002) Ancient phylogenetic relationships. Theor Popul Biol 61: 391-408. doi:10.1006/tpbi.2002.1593. PubMed: 12167360.
    • (2002) Theor Popul Biol , vol.61 , pp. 391-408
    • Gribaldo, S.1    Philippe, H.2
  • 67
    • 12444313041 scopus 로고    scopus 로고
    • Identifying and removing fast-evolving sites using compatibility analysis: An example from the arthropoda
    • doi:10.1080/10635150490888877. PubMed: 15764565
    • Pisani D (2004) Identifying and removing fast-evolving sites using compatibility analysis: an example from the arthropoda. Syst Biol 53: 978-989. doi:10.1080/10635150490888877. PubMed: 15764565.
    • (2004) Syst Biol , vol.53 , pp. 978-989
    • Pisani, D.1
  • 68
    • 84555190271 scopus 로고    scopus 로고
    • Difficult phylogenetic questions: More data, maybe; better methods, certainly
    • doi: 10.1186/1741-7007-9-91. PubMed: 22206462
    • Philippe H, Roure B (2011) Difficult phylogenetic questions: more data, maybe; better methods, certainly. BMC Biol 9: 91. doi: 10.1186/1741-7007-9-91. PubMed: 22206462.
    • (2011) BMC Biol , vol.9 , pp. 91
    • Philippe, H.1    Roure, B.2
  • 69
    • 1842431898 scopus 로고    scopus 로고
    • Ferns diversified in the shadow of angiosperms
    • doi:10.1038/nature02361. PubMed: 15058303
    • Schneider H, Schuettpelz E, Pryer KM, Cranfill R, Magallón S et al. (2004) Ferns diversified in the shadow of angiosperms. Nature 428: 553-557. doi:10.1038/nature02361. PubMed: 15058303.
    • (2004) Nature , vol.428 , pp. 553-557
    • Schneider, H.1    Schuettpelz, E.2    Pryer, K.M.3    Cranfill, R.4    Magallón, S.5
  • 70
    • 77950543389 scopus 로고    scopus 로고
    • An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants
    • doi:10.1073/pnas.1001225107. PubMed: 20304790
    • Smith SA, Beaulieu JM, Donoghue MJ (2010) An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants. Proc Natl Acad Sci U S A 107: 5897-5902. doi:10.1073/pnas.1001225107. PubMed: 20304790.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 5897-5902
    • Smith, S.A.1    Beaulieu, J.M.2    Donoghue, M.J.3
  • 71
    • 80052346740 scopus 로고    scopus 로고
    • Establishing a time-scale for plant evolution
    • doi:10.1111/j.1469-8137.2011.03794.x. PubMed: 21729086
    • Clarke JT, Warnock RCM, Donoghue PCJ (2011) Establishing a time-scale for plant evolution. New Phytol 192: 266-301. doi:10.1111/j.1469-8137.2011.03794.x. PubMed: 21729086.
    • (2011) New Phytol , vol.192 , pp. 266-301
    • Clarke, J.T.1    Warnock, R.C.M.2    Donoghue, P.C.J.3
  • 72
    • 84874918225 scopus 로고    scopus 로고
    • Land plant evolutionary timeline: Gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates
    • doi:10.3732/ajb.1200416. PubMed: 23445823
    • Magallón S, Hilu KW, Quandt D (2013) Land plant evolutionary timeline: gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates. Am J Bot 100: 556-573. doi:10.3732/ajb.1200416. PubMed: 23445823.
    • (2013) Am J Bot , vol.100 , pp. 556-573
    • Magallón, S.1    Hilu, K.W.2    Quandt, D.3
  • 73
    • 0037214757 scopus 로고    scopus 로고
    • An index of substitution saturation and its application
    • doi: 10.1016/S1055-7903(02)00326-3. PubMed: 12470932
    • Xia X, Xie Z, Salemi M, Chen L, Wang Y (2003) An index of substitution saturation and its application. Mol Phylogenet Evol 26: 1-7. doi: 10.1016/S1055-7903(02)00326-3. PubMed: 12470932.
    • (2003) Mol Phylogenet Evol , vol.26 , pp. 1-7
    • Xia, X.1    Xie, Z.2    Salemi, M.3    Chen, L.4    Wang, Y.5
  • 74
    • 0027470362 scopus 로고
    • The evolutionary history of the seed plant male gametophyte
    • doi: 10.1016/0169-5347(93)90125-9. PubMed: 21236093
    • Friedman WE (1993) The evolutionary history of the seed plant male gametophyte. Trends Ecol Evol 8: 15-21. doi: 10.1016/0169-5347(93)90125-9. PubMed: 21236093.
    • (1993) Trends Ecol Evol , vol.8 , pp. 15-21
    • Friedman, W.E.1
  • 75
    • 0141726796 scopus 로고    scopus 로고
    • Cycads: Evolutionary innovations and the role of plant-derived neurotoxins
    • doi:10.1016/S1360-1385(03)00190-0. PubMed: 13678912
    • Brenner ED, Stevenson DW, Twigg RW (2003) Cycads: evolutionary innovations and the role of plant-derived neurotoxins. Trends Plant Sci 8: 446-452. doi:10.1016/S1360-1385(03)00190-0. PubMed: 13678912.
    • (2003) Trends Plant Sci , vol.8 , pp. 446-452
    • Brenner, E.D.1    Stevenson, D.W.2    Twigg, R.W.3
  • 76
    • 14244261849 scopus 로고    scopus 로고
    • Comparative development of the spermatozoids of cycads and Ginkgo biloba
    • Available online at: 10.1663/0006-8101(2004)070[0005:CDOTSO]2.0.CO;2
    • Norstog KJ, Gifford EM, Stevenson DW (2004) Comparative development of the spermatozoids of cycads and Ginkgo biloba. Bot Rev 70: 5-15. Available online at: 10.1663/0006-8101(2004)070[0005:CDOTSO]2.0.CO;2
    • (2004) Bot Rev , vol.70 , pp. 5-15
    • Norstog, K.J.1    Gifford, E.M.2    Stevenson, D.W.3
  • 77
    • 76749096782 scopus 로고    scopus 로고
    • Defining the limits of flowers: The challenge of distinguishing between the evolutionary products of simple versus compound strobili
    • doi:10.1098/rstb.2009.0234. PubMed: 20047867
    • Rudall PJ, Bateman RM (2010) Defining the limits of flowers: the challenge of distinguishing between the evolutionary products of simple versus compound strobili. Philos Trans R Soc Lond B Biol Sci 365: 397-409. doi:10.1098/rstb.2009.0234. PubMed: 20047867.
    • (2010) Philos Trans R Soc Lond B Biol Sci , vol.365 , pp. 397-409
    • Rudall, P.J.1    Bateman, R.M.2
  • 78
    • 80052018698 scopus 로고    scopus 로고
    • An embryological study and systematic significance of the primitive gymnosperm Ginkgo biloba
    • doi:10.1111/j.1759-6831.2011.00123.x
    • Wang L, Wang D, Lin MM, Lu Y, Jiang XX et al. (2011) An embryological study and systematic significance of the primitive gymnosperm Ginkgo biloba. J Syst Evol 49: 353-361. doi:10.1111/j.1759-6831.2011.00123.x.
    • (2011) J Syst Evol , vol.49 , pp. 353-361
    • Wang, L.1    Wang, D.2    Lin, M.M.3    Lu, Y.4    Jiang, X.X.5
  • 79
    • 81055156928 scopus 로고    scopus 로고
    • Cenozoic extinctions account for the low diversity of extant gymnosperms compared with angiosperms
    • doi:10.1111/j.1469-8137.2011.03862.x. PubMed: 21895664
    • Crisp MD, Cook LG (2011) Cenozoic extinctions account for the low diversity of extant gymnosperms compared with angiosperms. New Phytol 192: 997-1009. doi:10.1111/j.1469-8137.2011.03862.x. PubMed: 21895664.
    • (2011) New Phytol , vol.192 , pp. 997-1009
    • Crisp, M.D.1    Cook, L.G.2
  • 80
    • 13244256972 scopus 로고    scopus 로고
    • prot4EST: Translating expressed sequence tags from neglected genomes
    • doi:10.1186/1471-2105-5-187. PubMed: 15571632
    • Wasmuth JD, Blaxter ML (2004) prot4EST: translating expressed sequence tags from neglected genomes. BMC Bioinformatics 5: 187. doi:10.1186/1471-2105-5- 187. PubMed: 15571632.
    • (2004) BMC Bioinformatics , vol.5 , pp. 187
    • Wasmuth, J.D.1    Blaxter, M.L.2
  • 81
    • 42149157760 scopus 로고    scopus 로고
    • Broad phylogenomic sampling improves resolution of the animal tree of life
    • doi:10.1038/nature06614. PubMed: 18322464
    • Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE et al. (2008) Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452: 745-749. doi:10.1038/nature06614. PubMed: 18322464.
    • (2008) Nature , vol.452 , pp. 745-749
    • Dunn, C.W.1    Hejnol, A.2    Matus, D.Q.3    Pang, K.4    Browne, W.E.5
  • 82
    • 72749099971 scopus 로고    scopus 로고
    • Assessing the root of bilaterian animals with scalable phylogenomic methods
    • doi:10.1098/rspb.2009.0896. PubMed: 19759036
    • Hejnol A, Obst M, Stamatakis A, Ott M, Rouse GW et al. (2009) Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc Biol Sci 276: 4261-4270. doi:10.1098/rspb.2009.0896. PubMed: 19759036.
    • (2009) Proc Biol Sci , vol.276 , pp. 4261-4270
    • Hejnol, A.1    Obst, M.2    Stamatakis, A.3    Ott, M.4    Rouse, G.W.5
  • 83
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • doi:10.1016/S0022-2836(05)80360-2. PubMed: 2231712
    • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410. doi:10.1016/S0022-2836(05)80360- 2. PubMed: 2231712.
    • (1990) J Mol Biol , vol.215 , pp. 403-410
    • Altschul, S.F.1    Gish, W.2    Miller, W.3    Myers, E.W.4    Lipman, D.J.5
  • 84
    • 19444363142 scopus 로고    scopus 로고
    • Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species
    • doi:10.1007/BF02715890. PubMed: 15876584
    • Liu QP, Xue QZ (2005) Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species. J Genet 84: 55-62. doi:10.1007/BF02715890. PubMed: 15876584.
    • (2005) J Genet , vol.84 , pp. 55-62
    • Liu, Q.P.1    Xue, Q.Z.2
  • 85
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • doi: 10.1093/nar/gkh340. PubMed: 15034147
    • Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797. doi: 10.1093/nar/gkh340. PubMed: 15034147.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 86
    • 67650757433 scopus 로고    scopus 로고
    • trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses
    • doi:10.1093/bioinformatics/btp348. PubMed: 19505945
    • Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25: 1972-1973. doi:10.1093/bioinformatics/ btp348. PubMed: 19505945.
    • (2009) Bioinformatics , vol.25 , pp. 1972-1973
    • Capella-Gutiérrez, S.1    Silla-Martínez, J.M.2    Gabaldón, T.3
  • 87
    • 84862777561 scopus 로고    scopus 로고
    • A genome triplication associated with early diversification of the core eudicots
    • doi:10.1186/gb-2012-13-1-r3. PubMed: 22280555
    • Jiao Y, Leebens-Mack J, Ayyampalayam S, Bowers JE, McKain MR et al. (2012) A genome triplication associated with early diversification of the core eudicots. Genome Biol 13: R3. doi:10.1186/gb-2012-13-1-r3. PubMed: 22280555.
    • (2012) Genome Biol , vol.13
    • Jiao, Y.1    Leebens-Mack, J.2    Ayyampalayam, S.3    Bowers, J.E.4    McKain, M.R.5
  • 88
    • 33747847779 scopus 로고    scopus 로고
    • PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments
    • doi:10.1093/nar/gkl315. PubMed: 16845082
    • Suyama M, Torrents D, Bork P (2006) PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 34: W609-W612. doi:10.1093/nar/gkl315. PubMed: 16845082.
    • (2006) Nucleic Acids Res , vol.34
    • Suyama, M.1    Torrents, D.2    Bork, P.3
  • 89
    • 40049112246 scopus 로고    scopus 로고
    • Phyutility: A phyloinformatics tool for trees, alignments and molecular data
    • doi: 10.1093/bioinformatics/btm619. PubMed: 18227120
    • Smith SA, Dunn CW (2008) Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics 24: 715-716. doi: 10.1093/bioinformatics/btm619. PubMed: 18227120.
    • (2008) Bioinformatics , vol.24 , pp. 715-716
    • Smith, S.A.1    Dunn, C.W.2
  • 90
    • 77951961553 scopus 로고    scopus 로고
    • Phybase: An R package for species tree analysis
    • doi:10.1093/bioinformatics/btq062. PubMed: 20156990
    • Liu L, Yu L (2010) Phybase: an R package for species tree analysis. Bioinformatics 26: 962-963. doi:10.1093/bioinformatics/btq062. PubMed: 20156990.
    • (2010) Bioinformatics , vol.26 , pp. 962-963
    • Liu, L.1    Yu, L.2
  • 91
    • 38149079760 scopus 로고    scopus 로고
    • Testing regions with nonsmooth boundaries via multiscale bootstrap
    • doi:10.1016/j.jspi.2007.04.001
    • Shimodaira H (2008) Testing regions with nonsmooth boundaries via multiscale bootstrap. J Stat Plan Infer 138: 1227-1241. doi:10.1016/j.jspi.2007. 04.001.
    • (2008) J Stat Plan Infer , vol.138 , pp. 1227-1241
    • Shimodaira, H.1
  • 92
    • 0034848170 scopus 로고    scopus 로고
    • DAMBE: Software package for data analysis in molecular biology and evolution
    • doi:10.1093/jhered/92.4.371. PubMed: 11535656
    • Xia X, Xie Z (2001) DAMBE: software package for data analysis in molecular biology and evolution. J Hered 92: 371-373. doi:10.1093/jhered/92.4. 371. PubMed: 11535656.
    • (2001) J Hered , vol.92 , pp. 371-373
    • Xia, X.1    Xie, Z.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.