-
1
-
-
70350218974
-
An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III
-
APG III
-
APG III. 2009. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot. J. Linn. Soc. 161:105-121.
-
(2009)
Bot. J. Linn. Soc.
, vol.161
, pp. 105-121
-
-
-
2
-
-
84873541206
-
An updated tribal and subtribal classification for the Bambusoideae (Poaceae)
-
Gielis J., Potters G., editors Belgium: World Bamboo Organization
-
th World Bamboo Congress, Antwerp, Belgium: World Bamboo Organization. p. 3-27.
-
(2012)
th World Bamboo Congress, Antwerp
, pp. 3-27
-
-
-
3
-
-
84872558507
-
Plastid genomes and deep relationships among the commelinid monocot angiosperms
-
Barrett C.F., Davis J.I., Leebens-Mack J., Conran J.G., Stevenson D.W. 2013. Plastid genomes and deep relationships among the commelinid monocot angiosperms. Cladistics 29:65-87.
-
(2013)
Cladistics
, vol.29
, pp. 65-87
-
-
Barrett, C.F.1
Davis, J.I.2
Leebens-Mack, J.3
Conran, J.G.4
Stevenson, D.W.5
-
4
-
-
20444491634
-
A review of long-branch attraction
-
Bergsten J. 2005. A review of long-branch attraction. Cladistics 21:163-193.
-
(2005)
Cladistics
, vol.21
, pp. 163-193
-
-
Bergsten, J.1
-
6
-
-
0020541784
-
An approach to population and evolutionary genetic theory for genes in mitochondria and chloroplasts, and some results
-
Birky C.W. Jr., Maruyama T., Fuerst P. 1983. An approach to population and evolutionary genetic theory for genes in mitochondria and chloroplasts, and some results. Genetics 103:513-527.
-
(1983)
Genetics
, vol.103
, pp. 513-527
-
-
Birky, C.W.1
Maruyama, T.2
Fuerst, P.3
-
7
-
-
43049120571
-
Large multi-gene phylogenetic trees of the grasses (Poaceae): Progress towards complete tribal and generic level sampling
-
Bouchenak-Khelladi Y., Salamin N., Savolainen V., Forest F., vander Bank M., Chase M.W., Hodkinson T.R. 2008. Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling. Mol. Phylogenet. Evol. 47:488-505.
-
(2008)
Mol. Phylogenet. Evol.
, vol.47
, pp. 488-505
-
-
Bouchenak-Khelladi, Y.1
Salamin, N.2
Savolainen, V.3
Forest, F.4
Vander Bank, M.5
Chase, M.W.6
Hodkinson, T.R.7
-
8
-
-
77952787167
-
Biogeography of the grasses (Poaceae): A phylogenetic approach to reveal evolutionary history in geographical space and ecological time
-
Bouchenak-Khelladi Y., Verboom G.A., Savolainen V., Hodkinson T.R. 2010. Biogeography of the grasses (Poaceae): a phylogenetic approach to reveal evolutionary history in geographical space and ecological time. Bot. J. Linn. Soc. 162:543-557.
-
(2010)
Bot. J. Linn. Soc.
, vol.162
, pp. 543-557
-
-
Bouchenak-Khelladi, Y.1
Verboom, G.A.2
Savolainen, V.3
Hodkinson, T.R.4
-
9
-
-
9944255059
-
Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards
-
Brandley M.C., Schmitz A., Reeder T.W. 2005. Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Syst. Biol. 54:373-390.
-
(2005)
Syst. Biol.
, vol.54
, pp. 373-390
-
-
Brandley, M.C.1
Schmitz, A.2
Reeder, T.W.3
-
10
-
-
37249003697
-
The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics
-
Brown J.M., Lemmon A.R. 2007. The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics. Syst. Biol. 56:643-655.
-
(2007)
Syst. Biol.
, vol.56
, pp. 643-655
-
-
Brown, J.M.1
Lemmon, A.R.2
-
11
-
-
84875125807
-
Plastome sequences of two new world bamboos-Arundinaria gigantea and Cryptochloa strictiflora (Poaceae)-extended phylogenomic understanding of Bambusoideae
-
Burke S.V., Grennan C.P., Duvall M.R. 2012. Plastome sequences of two new world bamboos-Arundinaria gigantea and Cryptochloa strictiflora (Poaceae)-extended phylogenomic understanding of Bambusoideae. Am. J. Bot. 99:1951-1961.
-
(2012)
Am. J. Bot.
, vol.99
, pp. 1951-1961
-
-
Burke, S.V.1
Grennan, C.P.2
Duvall, M.R.3
-
12
-
-
79951569533
-
Genome-scale phylogenetics: Inferring the plant Tree of Life from 18,896 gene trees
-
Burlerigh J.G., Bansal M.S., Eulenstein O., Hartmann S., Wehe A., Vision T.J. 2011. Genome-scale phylogenetics: inferring the plant Tree of Life from 18,896 gene trees. Syst. Biol. 60:117-125.
-
(2011)
Syst. Biol.
, vol.60
, pp. 117-125
-
-
Burlerigh, J.G.1
Bansal, M.S.2
Eulenstein, O.3
Hartmann, S.4
Wehe, A.5
Vision, T.J.6
-
14
-
-
84928324810
-
-
Beijing: Science Press
-
Chen R.Y., Li X.L., Song W.Q., Liang G.L., Zhang P.X., Lin R.S., Zong W.X., Chen C.B., Feng X.L. 2003. Chromosome atlas of various bamboo species. Chromosome atlas of major economic plants genome in China IV. Beijing: Science Press.
-
(2003)
Chromosome Atlas of Various Bamboo Species. Chromosome Atlas of Major Economic Plants Genome in China IV.
-
-
Chen, R.Y.1
Li, X.L.2
Song, W.Q.3
Liang, G.L.4
Zhang, P.X.5
Lin, R.S.6
Zong, W.X.7
Chen, C.B.8
Feng, X.L.9
-
17
-
-
17744394753
-
Phylogenomics and the reconstruction of the tree of life
-
Delsuc F., Brinkmann H., Philippe H. 2005. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet. 6:361-375.
-
(2005)
Nat. Rev. Genet.
, vol.6
, pp. 361-375
-
-
Delsuc, F.1
Brinkmann, H.2
Philippe, H.3
-
18
-
-
85006630248
-
A rapid DNA isolation procedure for small quantities of fresh leaf tissue
-
Doyle J.J., Doyle J.L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19:11-15.
-
(1987)
Phytochem. Bull.
, vol.19
, pp. 11-15
-
-
Doyle, J.J.1
Doyle, J.L.2
-
19
-
-
84860139764
-
Multiple continental radiations and correlates of diversification in Lupinus (Leguminosae): Testing for key innovation with incomplete taxon sampling
-
Drummond C.S., Eastwood R.J., Miotto S.T.S., Hughes C.E. 2012. Multiple continental radiations and correlates of diversification in Lupinus (Leguminosae): testing for key innovation with incomplete taxon sampling. Syst. Biol. 61:443-460.
-
(2012)
Syst. Biol.
, vol.61
, pp. 443-460
-
-
Drummond, C.S.1
Eastwood, R.J.2
Miotto, S.T.S.3
Hughes, C.E.4
-
20
-
-
84959798530
-
Cases in which parsimony or compatibility methods will be positively misleading
-
Felsenstein J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
-
(1978)
Syst. Zool.
, vol.27
, pp. 401-410
-
-
Felsenstein, J.1
-
21
-
-
19044400807
-
Molecular phylogeny of the Carnivora (Mammalia): Assessing the impact of increased sampling on resolving enigmatic relationships
-
Flynn J.J., Finarelli J.A., Zehr S., Hsu J., Nedbal M.A. 2005. Molecular phylogeny of the Carnivora (Mammalia): assessing the impact of increased sampling on resolving enigmatic relationships. Syst. Biol. 54:317-337.
-
(2005)
Syst. Biol.
, vol.54
, pp. 317-337
-
-
Flynn, J.J.1
Finarelli, J.A.2
Zehr, S.3
Hsu, J.4
Nedbal, M.A.5
-
22
-
-
33746252513
-
Chinese moso bamboo: Its importance
-
Fu J.H. 2001. Chinese moso bamboo: its importance. Bamboo 22:5-7.
-
(2001)
Bamboo
, vol.22
, pp. 5-7
-
-
Fu, J.H.1
-
23
-
-
0035619568
-
Genetic variation and evolution of the alpine bamboos (Poaceae: Bambusoideae) using DNA sequence data
-
Guo Z.H., Chen Y.Y., Li D.Z., Yang J.B. 2001. Genetic variation and evolution of the alpine bamboos (Poaceae: Bambusoideae) using DNA sequence data. J. Plant Res. 114:315-322.
-
(2001)
J. Plant Res.
, vol.114
, pp. 315-322
-
-
Guo, Z.H.1
Chen, Y.Y.2
Li, D.Z.3
Yang, J.B.4
-
24
-
-
0347093519
-
Phylogenetics of the Thamnocalamus group and its allies (Gramineae: Bambusoideae): Inference from the sequence of GBSSI gene and ITS spacer
-
Guo Z.H., Li D.Z. 2004. Phylogenetics of the Thamnocalamus group and its allies (Gramineae: Bambusoideae): inference from the sequence of GBSSI gene and ITS spacer. Mol. Phylogenet. Evol. 30:1-12.
-
(2004)
Mol. Phylogenet. Evol.
, vol.30
, pp. 1-12
-
-
Guo, Z.H.1
Li, D.Z.2
-
25
-
-
46449135061
-
A phylogenomic study of birds reveals their evolutionary history
-
Hackett S.J., Kimball R.T., Reddy S., Bowie R.C., Braun E.L., Braun M.J., Chojnowski J.L., Cox W.A., Han K.L., Harshman J., Huddleston C.J., Marks B.D., Miglia K.J., Moore W.S., Sheldon F.H., Steadman D.W., Wirr C.C., Yuri T. 2008. A phylogenomic study of birds reveals their evolutionary history. Science 320:1763-1768.
-
(2008)
Science
, vol.320
, pp. 1763-1768
-
-
Hackett, S.J.1
Kimball, R.T.2
Reddy, S.3
Bowie, R.C.4
Braun, E.L.5
Braun, M.J.6
Chojnowski, J.L.7
Cox, W.A.8
Han, K.L.9
Harshman, J.10
Huddleston, C.J.11
Marks, B.D.12
Miglia, K.J.13
Moore, W.S.14
Sheldon, F.H.15
Steadman, D.W.16
Wirr, C.C.17
Yuri, T.18
-
26
-
-
33747339757
-
Resolution of phylogenetic conflict in large data sets by increased taxon sampling
-
Hedtke S.M., Townsend T.M., Hillis D.M. 2006. Resolution of phylogenetic conflict in large data sets by increased taxon sampling. Syst. Biol. 55:522-529.
-
(2006)
Syst. Biol.
, vol.55
, pp. 522-529
-
-
Hedtke, S.M.1
Townsend, T.M.2
Hillis, D.M.3
-
27
-
-
78649570620
-
Phylogenetic analyses of plastid and nuclear DNA sequences indicate a rapid late Miocene radiation of the temperate bamboo tribe Arundinarieae (Poaceae, Bambusoideae)
-
Hodkinson T.R., Chonghaile G.N., Sungkaew S., Chase M.W., Salamin N., Stapleton C.M.A. 2010. Phylogenetic analyses of plastid and nuclear DNA sequences indicate a rapid late Miocene radiation of the temperate bamboo tribe Arundinarieae (Poaceae, Bambusoideae). Plant Ecol. Divers. 3:109-120.
-
(2010)
Plant Ecol. Divers.
, vol.3
, pp. 109-120
-
-
Hodkinson, T.R.1
Chonghaile, G.N.2
Sungkaew, S.3
Chase, M.W.4
Salamin, N.5
Stapleton, C.M.A.6
-
28
-
-
0032148641
-
Systematic bias in phylogenetic analysis: Is the Strepsiptera problem solved?
-
Huelsenbeck J.P. 1998. Systematic bias in phylogenetic analysis: is the Strepsiptera problem solved? Syst. Biol. 47:519-537.
-
(1998)
Syst. Biol.
, vol.47
, pp. 519-537
-
-
Huelsenbeck, J.P.1
-
29
-
-
30744470609
-
Application of phylogenetic networks in evolutionary studies
-
Huson D.H., Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23:254-267.
-
(2006)
Mol. Biol. Evol.
, vol.23
, pp. 254-267
-
-
Huson, D.H.1
Bryant, D.2
-
30
-
-
37649007931
-
Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns
-
Jansen R.K., Cai Z., Raubeson L.A., Daniell H., dePamphilis C.W., Leebens-Mack J., MÜller K.F., Guisinger-Bellian M., Haberle R.C., Hansen A.K., Chumley T.W., Lee S., Peery R., McNeal J.R., Kuehl J.V., Boore J.L. 2007. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc. Natl Acad. Sci. U. S.A. 104:19369-19374.
-
(2007)
Proc. Natl Acad. Sci. U. S.A.
, vol.104
, pp. 19369-19374
-
-
Jansen, R.K.1
Cai, Z.2
Raubeson, L.A.3
Daniell, H.4
DePamphilis, C.W.5
Leebens-Mack, J.6
Müller, K.F.7
Guisinger-Bellian, M.8
Haberle, R.C.9
Hansen, A.K.10
Chumley, T.W.11
Lee, S.12
Peery, R.13
McNeal, J.R.14
Kuehl, J.V.15
Boore, J.L.16
-
31
-
-
0000282967
-
Why bambooswait so long to flower
-
Janzen D.H. 1976.Why bambooswait so long to flower. Ann. Rev. Ecol. Syst. 7:347-391.
-
(1976)
Ann. Rev. Ecol. Syst.
, vol.7
, pp. 347-391
-
-
Janzen, D.H.1
-
33
-
-
45249124620
-
Resolving an ancient, rapid radiation in Saxifragales
-
Jian S., Soltis P.S., Gitzendanner M.A., Moore M.J., Li R., Hendry T.A., Qiu Y.L., Dhingra A., Bell C.D., Soltis D.E. 2008. Resolving an ancient, rapid radiation in Saxifragales. Syst. Biol. 57:38-57.
-
(2008)
Syst. Biol.
, vol.57
, pp. 38-57
-
-
Jian, S.1
Soltis, P.S.2
Gitzendanner, M.A.3
Moore, M.J.4
Li, R.5
Hendry, T.A.6
Qiu, Y.L.7
Dhingra, A.8
Bell, C.D.9
Soltis, D.E.10
-
34
-
-
13744252890
-
MAFFT version 5: Improvement in accuracy of multiple sequence alignment
-
Katoh K., Kuma K., Toh H., Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33:511-518.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.2
Toh, H.3
Miyata, T.4
-
35
-
-
84877928769
-
Higher level phylogenetic relationships within the bamboos (Poaceae: Bambusoideae) based on five plastid markers
-
Kelchner S.A., Bamboo Phylogeny Group. 2013. Higher level phylogenetic relationships within the bamboos (Poaceae: Bambusoideae) based on five plastid markers. Mol. Phylogenet. Evol. 67:404-413.
-
(2013)
Mol. Phylogenet. Evol.
, vol.67
, pp. 404-413
-
-
Kelchner, S.A.1
-
36
-
-
25144453704
-
Untangling long branches: Identifying conflicting phylogenetic signals using spectral analysis, neighbor-net, and consensus networks
-
Kennedy M., Holland B.R., Gray R.D., Spencer H.G. 2005. Untangling long branches: identifying conflicting phylogenetic signals using spectral analysis, neighbor-net, and consensus networks. Syst. Biol. 54:620-633.
-
(2005)
Syst. Biol.
, vol.54
, pp. 620-633
-
-
Kennedy, M.1
Holland, B.R.2
Gray, R.D.3
Spencer, H.G.4
-
37
-
-
84861380450
-
PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses
-
Lanfear R., Calcott B., Ho S.Y.W., Guindon S. 2012. PartitionFinder: combined selection of partitioning schemes and substitution 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
-
38
-
-
80755128987
-
Multilocus resolution of phylogeny and timescale in the extant adaptive radiation of Hawaiian honeycreepers
-
Lerner H.R.L., Meyer M., James H.F., Hofreiter M., Fleischer R.C. 2011. Multilocus resolution of phylogeny and timescale in the extant adaptive radiation of Hawaiian honeycreepers. Curr. Biol. 21:1838-1844.
-
(2011)
Curr. Biol.
, vol.21
, pp. 1838-1844
-
-
Lerner, H.R.L.1
Meyer, M.2
James, H.F.3
Hofreiter, M.4
Fleischer, R.C.5
-
39
-
-
47249090871
-
Optimal data partitioning and a test case for ray-finned fishes (Actinopterygii) based on ten nuclear loci
-
Li C., Lu G., Ortí G. 2008. Optimal data partitioning and a test case for ray-finned fishes (Actinopterygii) based on ten nuclear loci. Syst. Biol. 57:519-539.
-
(2008)
Syst. Biol.
, vol.57
, pp. 519-539
-
-
Li, C.1
Lu, G.2
Ortí, G.3
-
40
-
-
52249101125
-
Taxonomy and biogeography of the Bambuseae (Gramineae: Bambusoideae)
-
Rao A.N., Rao V.R., editors. Bamboo - Conservation, Diversity, Ecogeography, Germplasm, Resource Utilization and Taxonomy Serdang, Malaysia: IPGRI-APO
-
Li D.Z. 1999. Taxonomy and biogeography of the Bambuseae (Gramineae: Bambusoideae). In: Rao A.N., Rao V.R., editors. Bamboo - conservation, diversity, ecogeography, germplasm, resource utilization and taxonomy. Proceeding of training course cum workshop, Kunming and Xishuangbanna, Yunnan, China. Serdang, Malaysia: IPGRI-APO. p. 14-23.
-
(1999)
Proceeding of Training Course Cum Workshop, Kunming and Xishuangbanna, Yunnan, China
, pp. 14-23
-
-
Li, D.Z.1
-
41
-
-
84928328083
-
-
Wu Z.Y., Raven P.H., editors Beijing & St. Louis: Science Press & Missouri Botanical Garden Press
-
Li D.Z., Wang Z.P., Zhu Z.D., Xia N.H., Jia L.Z., Guo Z.H., Yang G.Y., Stapleton C. 2006. Bambuseae in Flora of China (Wu Z.Y., Raven P.H., editors.). Vol. 22. Beijing & St. Louis: Science Press & Missouri Botanical Garden Press.
-
(2006)
Bambuseae in Flora of China
, vol.22
-
-
Li, D.Z.1
Wang, Z.P.2
Zhu, Z.D.3
Xia, N.H.4
Jia, L.Z.5
Guo, Z.H.6
Yang, G.Y.7
Stapleton, C.8
-
42
-
-
75649124547
-
De novo assembly of human genomes with massively parallel short read sequencing
-
Li R., Zhu H., Ruan J., Qian W., Fang X., Shi Z., Li Y., Li S., Shan G., Kristiansen K., Li S., Yang H., Wang J., Wang J. 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20:265-272.
-
(2010)
Genome Res.
, vol.20
, pp. 265-272
-
-
Li, R.1
Zhu, H.2
Ruan, J.3
Qian, W.4
Fang, X.5
Shi, Z.6
Li, Y.7
Li, S.8
Shan, G.9
Kristiansen, K.10
Li, S.11
Yang, H.12
Wang, J.13
Wang, J.14
-
43
-
-
72049096137
-
Cryptic failure if partitioned Bayesian phylogenetic analyses: Lost in the land of long trees
-
Marshall D.C. 2010.Cryptic failure if partitioned Bayesian phylogenetic analyses: lost in the land of long trees. Syst. Biol. 59:108-117.
-
(2010)
Syst. Biol.
, vol.59
, pp. 108-117
-
-
Marshall, D.C.1
-
44
-
-
0003752385
-
-
Cambridge: Harvard University Press. [Reprint 1993, Washington DC: Smithsonian Institution Press.]
-
McClure F.A. 1973. The Bamboos: a fresh perspective. Cambridge: Harvard University Press. [Reprint 1993, Washington DC: Smithsonian Institution Press.]
-
(1973)
The Bamboos: A Fresh Perspective.
-
-
McClure, F.A.1
-
45
-
-
37549054628
-
Using plastid genome-scale data to resolve enigmatic relationships among the basal angiosperms
-
Moore M.J., Bell C.D., Soltis P.S., Soltis D.E. 2007. Using plastid genome-scale data to resolve enigmatic relationships among the basal angiosperms. Proc. Natl Acad. Sci. U. S. A. 104:19363-19368.
-
(2007)
Proc. Natl Acad. Sci. U. S. A.
, vol.104
, pp. 19363-19368
-
-
Moore, M.J.1
Bell, C.D.2
Soltis, P.S.3
Soltis, D.E.4
-
46
-
-
77949494249
-
Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots
-
Moore M.J., Soltis P.S., Bell C.D., Burleigh J.G., Soltis D.E. 2010. Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots. Proc. Natl Acad. Sci. U. S. A. 107:4623-4628.
-
(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
-
47
-
-
84862858217
-
Phylogeny and biogeography of the core babblers (Aves: Timaliidae)
-
Moyle R.G., Andersen M.J., Oliveros C.H., Steinheimer F.D., Reddy S. 2012. Phylogeny and biogeography of the core babblers (Aves: Timaliidae). Syst. Biol. 61:631-651.
-
(2012)
Syst. Biol.
, vol.61
, pp. 631-651
-
-
Moyle, R.G.1
Andersen, M.J.2
Oliveros, C.H.3
Steinheimer, F.D.4
Reddy, S.5
-
49
-
-
39149141072
-
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
-
51
-
-
0022294484
-
Comparative organization of chloroplast genomes
-
Palmer J.D. 1985. Comparative organization of chloroplast genomes. Annu. Rev. Genet. 19:325-354.
-
(1985)
Annu. Rev. Genet.
, vol.19
, pp. 325-354
-
-
Palmer, J.D.1
-
52
-
-
72549096467
-
Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes
-
Parks M., Cronn R., Liston A. 2009. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biol. 7:84.
-
(2009)
BMC Biol.
, vol.7
, pp. 84
-
-
Parks, M.1
Cronn, R.2
Liston, A.3
-
53
-
-
52249112021
-
Highly heterogeneous generic delimitation within the temperate bamboo clade (Poaceae: Bambusoideae): Evidence from GBSSI and ITS sequences
-
Peng S., Yang H.Q., Li D.Z. 2008. Highly heterogeneous generic delimitation within the temperate bamboo clade (Poaceae: Bambusoideae): evidence from GBSSI and ITS sequences. Taxon 57:799-810.
-
(2008)
Taxon
, vol.57
, pp. 799-810
-
-
Peng, S.1
Yang, H.Q.2
Li, D.Z.3
-
54
-
-
79953716259
-
Resolving difficult phylogenetic questions: Why more sequences are not enough
-
Philippe H., Brinkman H., Lavrov D.V., Littlewood D.T.J., Manuel M., Wörheide G., Baurain D. 2011. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol. 9:e1000602.
-
(2011)
PLoS Biol.
, vol.9
, pp. e1000602
-
-
Philippe, H.1
Brinkman, H.2
Lavrov, D.V.3
Littlewood, D.T.J.4
Manuel, M.5
Wörheide, G.6
Baurain, D.7
-
55
-
-
9644301241
-
Model selection and model averaging in phylogenetics: Advantages of Akaike Information Criterion and Bayesian approaches over likelihood ratio tests
-
Posada D., Buckley T.R. 2004. Model selection and model averaging in phylogenetics: advantages of Akaike Information Criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 53:793-808.
-
(2004)
Syst. Biol.
, vol.53
, pp. 793-808
-
-
Posada, D.1
Buckley, T.R.2
-
56
-
-
0031773680
-
Modeltest: Testing the model of DNA substitution
-
Posada D., Crandall K.A. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818.
-
(1998)
Bioinformatics
, vol.14
, pp. 817-818
-
-
Posada, D.1
Crandall, K.A.2
-
58
-
-
0030928378
-
Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
-
Rambaut A., Grassly N.C. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238.
-
(1997)
Comput. Appl. Biosci.
, vol.13
, pp. 235-238
-
-
Rambaut, A.1
Grassly, N.C.2
-
59
-
-
33751039720
-
Bushes in the tree of life
-
Rokas A., Carroll S.B. 2006. Bushes in the tree of life. PLoS Biol. 4:e352.
-
(2006)
PLoS Biol.
, vol.4
, pp. e352
-
-
Rokas, A.1
Carroll, S.B.2
-
60
-
-
0041386108
-
MRBAYES 3: Bayesian phylogenetic inference under mixed models
-
Ronquist F., Huelsenbeck J.P. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
-
(2003)
Bioinformatics
, vol.19
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.P.2
-
61
-
-
0035845536
-
Incomplete taxon sampling is not a problem for phylogenetic inference
-
Rosenberg M.S., Kumar S. 2001. Incomplete taxon sampling is not a problem for phylogenetic inference. Proc. Natl Acad. Sci. U. S. A. 98:10751-10756.
-
(2001)
Proc. Natl Acad. Sci. U. S. A.
, vol.98
, pp. 10751-10756
-
-
Rosenberg, M.S.1
Kumar, S.2
-
62
-
-
84862889898
-
Biogeography and divergence time estimates of woody bamboos: Insights in the evolution of neotropical bamboos
-
Ruiz-Sanchez E. 2011. Biogeography and divergence time estimates of woody bamboos: insights in the evolution of neotropical bamboos. Bol. Soc. Bot. Mex. 88:67-75.
-
(2011)
Bol. Soc. Bot. Mex.
, vol.88
, pp. 67-75
-
-
Ruiz-Sanchez, E.1
-
63
-
-
79955373147
-
Causes of plant diversification in the cape biodiversity hotspot of South Africa
-
Schnitzler J., Barraclough T.G., Boatwright J.S., Goldblatt P., Manning J.C., Powell M.P., Rebelo T., Savolainen V. 2011. Causes of plant diversification in the cape biodiversity hotspot of South Africa. Syst. Biol. 60:343-357.
-
(2011)
Syst. Biol.
, vol.60
, pp. 343-357
-
-
Schnitzler, J.1
Barraclough, T.G.2
Boatwright, J.S.3
Goldblatt, P.4
Manning, J.C.5
Powell, M.P.6
Rebelo, T.7
Savolainen, V.8
-
64
-
-
53649106195
-
Next-generation DNA sequencing
-
Shendure J., Ji H. 2008. Next-generation DNA sequencing. Nat. Biotechnol. 26:1135-1145.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1135-1145
-
-
Shendure, J.1
Ji, H.2
-
65
-
-
0036623258
-
An approximately unbiased test of phylogenetic tree selection
-
Shimodaira H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51:492-508.
-
(2002)
Syst. Biol.
, vol.51
, pp. 492-508
-
-
Shimodaira, H.1
-
66
-
-
0036139287
-
CONSEL: For assessing the confidence of phylogenetic tree selection
-
Shimodaira H., Hasewaga M. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246-1247.
-
(2001)
Bioinformatics
, vol.17
, pp. 1246-1247
-
-
Shimodaira, H.1
Hasewaga, M.2
-
67
-
-
84863337944
-
Angiosperm phylogeny: 17 genes, 640 taxa
-
Soltis D.E., Smith S.A., Cellinese N., Wurdack K.J., Tank D.C., Brockington S.F., Refulio-Rodriguez N.F., Walker J.B., Moore M.J., Carlsward B.S., Bell C.D., Latvis M., Crawley S., Black C., Diouf D., Xi Z., Rushworth C.A., Gitzendanner M.A., Sytsma K.J., Qiu Y.L., Hilu K.W., Davis C.C., Sanderson M.J., Beaman R.S., Olmstead R.G., JuddW.S., Donoghue M.J., Soltis P.S. 2011. Angiosperm phylogeny: 17 genes, 640 taxa. Am. J. Bot. 98:704-730.
-
(2011)
Am. J. Bot.
, vol.98
, pp. 704-730
-
-
Soltis, D.E.1
Smith, S.A.2
Cellinese, N.3
Wurdack, K.J.4
Tank, D.C.5
Brockington, S.F.6
Refulio-Rodriguez, N.F.7
Walker, J.B.8
Moore, M.J.9
Carlsward, B.S.10
Bell, C.D.11
Latvis, M.12
Crawley, S.13
Black, C.14
Diouf, D.15
Xi, Z.16
Rushworth, C.A.17
Gitzendanner, M.A.18
Sytsma, K.J.19
Qiu, Y.L.20
Hilu, K.W.21
Davis, C.C.22
Sanderson, M.J.23
Beaman, R.S.24
Olmstead, R.G.25
Judd, W.S.26
Donoghue, M.J.27
Soltis, P.S.28
more..
-
68
-
-
33750403801
-
RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
-
(2006)
Bioinformatics
, vol.22
, pp. 2688-2690
-
-
Stamatakis, A.1
-
69
-
-
84904437205
-
Bergbambos and Oldeania, newgenera of African bamboos (Poaceae, Bambusoideae)
-
Stapleton C.M.A. 2013. Bergbambos and Oldeania, newgenera of African bamboos (Poaceae, Bambusoideae). PhytoKeys 25:87-103.
-
(2013)
PhytoKeys
, vol.25
, pp. 87-103
-
-
Stapleton, C.M.A.1
-
70
-
-
58149386206
-
Nonmonophyly of the woody bamboos (Bambuseae; Poaceae): A multigene region phylogenetic analysis of Bambusoideae s.s.
-
Sungkaew S., Stapleton C.M.A., Salamin N., Hodkinson T.R. 2009.Nonmonophyly of the woody bamboos (Bambuseae; Poaceae): a multigene region phylogenetic analysis of Bambusoideae s.s. J. Plant Res. 122:95-108.
-
(2009)
J. Plant Res.
, vol.122
, pp. 95-108
-
-
Sungkaew, S.1
Stapleton, C.M.A.2
Salamin, N.3
Hodkinson, T.R.4
-
72
-
-
34547781750
-
MEGA 4: Molecular evolutionary genetics analysis (MEGA) software version 4.0
-
Tamura K., Dudley J., Nei M., Kumar S. 2007. MEGA 4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 1596-1599
-
-
Tamura, K.1
Dudley, J.2
Nei, M.3
Kumar, S.4
-
73
-
-
77953325693
-
Phylogeny of the temperate bamboos (Poaceae: Bambusoideae: Bambuseae) with an emphasis on Arundinaria and allies
-
Triplett J.K., Clark L.G. 2010. Phylogeny of the temperate bamboos (Poaceae: Bambusoideae: Bambuseae) with an emphasis on Arundinaria and allies. Syst. Bot. 35:102-120.
-
(2010)
Syst. Bot.
, vol.35
, pp. 102-120
-
-
Triplett, J.K.1
Clark, L.G.2
-
74
-
-
77952710892
-
Unparalleled rates of species diversification in Europe
-
Valente L.M., Savolainen V., VargasP. 2010. Unparalleled rates of species diversification in Europe. Proc. R. Soc. B 277:1489-1496.
-
(2010)
Proc. R. Soc. B
, vol.277
, pp. 1489-1496
-
-
Valente, L.M.1
Savolainen, V.2
Vargas, P.3
-
75
-
-
77950850793
-
Phylogeny and biogeography of Dolichoderine ants: Effects of data partitioning and relict taxa on historical inference
-
Ward P.S., Brady S.G., Fisher B.L., Schultz T.R. 2010. Phylogeny and biogeography of Dolichoderine ants: effects of data partitioning and relict taxa on historical inference. Syst. Biol. 59:342-362.
-
(2010)
Syst. Biol.
, vol.59
, pp. 342-362
-
-
Ward, P.S.1
Brady, S.G.2
Fisher, B.L.3
Schultz, T.R.4
-
76
-
-
61349128420
-
Phylogeny, species richness, and ecological specialization in Cyperaceae tribe Cariceae
-
Waterway M., Hoshino T., Masaki T. 2009. Phylogeny, species richness, and ecological specialization in Cyperaceae tribe Cariceae. Bot. Rev. 75:138-159.
-
(2009)
Bot. Rev.
, vol.75
, pp. 138-159
-
-
Waterway, M.1
Hoshino, T.2
Masaki, T.3
-
79
-
-
43749109878
-
Branch length, support, and congruence: Testing the phylogenomic approach with 20 nuclear loci in snakes
-
Wiens J.J., Kuczynski C.A., Smith S.A., Mulcahy D.G., Sites J.W., Townsend T.M., Reeder T.W. 2008. Branch length, support, and congruence: testing the phylogenomic approach with 20 nuclear loci in snakes. Syst. Biol. 57:420-431.
-
(2008)
Syst. Biol.
, vol.57
, pp. 420-431
-
-
Wiens, J.J.1
Kuczynski, C.A.2
Smith, S.A.3
Mulcahy, D.G.4
Sites, J.W.5
Townsend, T.M.6
Reeder, T.W.7
-
80
-
-
69149092980
-
Complete nucleotide sequence of Dendrocalamus latiflorus and Bambusa oldhamii chloroplast genomes
-
Wu F.H., Kan D.P., Lee S.B., Daniell H., Lee Y.W., Lin C.C., Lin N.S., Lin C.S. 2009. Complete nucleotide sequence of Dendrocalamus latiflorus and Bambusa oldhamii chloroplast genomes. Tree Physiol. 29:847-856.
-
(2009)
Tree Physiol.
, vol.29
, pp. 847-856
-
-
Wu, F.H.1
Kan, D.P.2
Lee, S.B.3
Daniell, H.4
Lee, Y.W.5
Lin, C.C.6
Lin, N.S.7
Lin, C.S.8
-
81
-
-
83655203406
-
The phylogeny of the BEP clade in grasses revisited: Evidence from the whole-genome sequences of chloroplast
-
Wu Z.Q., Ge S. 2012. The phylogeny of the BEP clade in grasses revisited: evidence from the whole-genome sequences of chloroplast. Mol. Phylogenet. Evol. 62:573-578.
-
(2012)
Mol. Phylogenet. Evol.
, vol.62
, pp. 573-578
-
-
Wu, Z.Q.1
Ge, S.2
-
82
-
-
10244240599
-
Automatic annotation of organellar genomes with DOGMA
-
Wyman S.K., Jansen R.K., Boore J.L. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252-3255.
-
(2004)
Bioinformatics
, vol.20
, pp. 3252-3255
-
-
Wyman, S.K.1
Jansen, R.K.2
Boore, J.L.3
-
83
-
-
84867919296
-
Phylogenomics and a posteriori data partitioning resolve theCretaceous angiospermradiation Malpighiales
-
Xi Z., Ruhfel B.R., Schaefer H., Amorim A.M., Sugumaran M., Wurdack K.J., Endress P.K., Matthews M.L., Stevens P.F., Mathews S., Davis C.C. 2012. Phylogenomics and a posteriori data partitioning resolve theCretaceous angiospermradiation Malpighiales. Proc. Natl Acad. Sci. U. S. A. 109:17519-17524.
-
(2012)
Proc. Natl Acad. Sci. U. S. A.
, vol.109
, pp. 17519-17524
-
-
Xi, Z.1
Ruhfel, B.R.2
Schaefer, H.3
Amorim, A.M.4
Sugumaran, M.5
Wurdack, K.J.6
Endress, P.K.7
Matthews, M.L.8
Stevens, P.F.9
Mathews, S.10
Davis, C.C.11
-
84
-
-
84878106037
-
The monophyly of Chimonocalamus and conflicting gene trees in Arundinarieae (Poaceae: Bambusoideae) inferred fromfour plastid and two nuclear markers
-
Yang H.M., Zhang Y.X., Yang J.B., Li D.Z. 2013. The monophyly of Chimonocalamus and conflicting gene trees in Arundinarieae (Poaceae: Bambusoideae) inferred fromfour plastid and two nuclear markers. Mol. Phylogenet. Evol. 68:340-356.
-
(2013)
Mol. Phylogenet. Evol.
, vol.68
, pp. 340-356
-
-
Yang, H.M.1
Zhang, Y.X.2
Yang, J.B.3
Li, D.Z.4
-
85
-
-
84905968819
-
Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs
-
Yang J.B., Li D.Z., Li H.T. 2014. Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs. Mol. Ecol. Resour. 14:1024-1031.
-
(2014)
Mol. Ecol. Resour.
, vol.14
, pp. 1024-1031
-
-
Yang, J.B.1
Li, D.Z.2
Li, H.T.3
-
86
-
-
77953325567
-
Large multi-locus plastid phylogeny of the tribe Arundinarieae (Poaceae: Bambusoideae) reveals tenmajor lineages and lowrate of molecular divergence
-
Zeng C.X., Zhang Y.X., Triplett J.K., Yang J.B., Li D.Z. 2010. Large multi-locus plastid phylogeny of the tribe Arundinarieae (Poaceae: Bambusoideae) reveals tenmajor lineages and lowrate of molecular divergence. Mol. Phylogenet. Evol. 56:821-839.
-
(2010)
Mol. Phylogenet. Evol.
, vol.56
, pp. 821-839
-
-
Zeng, C.X.1
Zhang, Y.X.2
Triplett, J.K.3
Yang, J.B.4
Li, D.Z.5
-
87
-
-
79957814250
-
High-throughput sequencing of six bamboo chloroplast genomes: Phylogenetic implications for temperate woody bamboos (Poaceae: Bambusoideae)
-
Zhang Y.J., Ma P.F., Li D.Z. 2011. High-throughput sequencing of six bamboo chloroplast genomes: phylogenetic implications for temperate woody bamboos (Poaceae: Bambusoideae). PLoS One 6:e20596.
-
(2011)
PLoS One
, vol.6
, pp. e20596
-
-
Zhang, Y.J.1
Ma, P.F.2
Li, D.Z.3
-
88
-
-
84862816178
-
Complex evolution in Arundinarieae (Poaceae: Bambusoideae): Incongruence between plastid and nuclear GBSSI gene phylogenies
-
Zhang Y.X., Zeng C.X., Li D.Z. 2012. Complex evolution in Arundinarieae (Poaceae: Bambusoideae): incongruence between plastid and nuclear GBSSI gene phylogenies. Mol. Phylogenet. Evol. 63:777-797.
-
(2012)
Mol. Phylogenet. Evol.
, vol.63
, pp. 777-797
-
-
Zhang, Y.X.1
Zeng, C.X.2
Li, D.Z.3
-
89
-
-
84555186853
-
Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the Laurasiatherian mammals
-
Zhou X., Xu S., Xu J., Chen B., Zhou K., Yang G. 2012. Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the Laurasiatherian mammals. Syst. Biol. 61:150-164.
-
(2012)
Syst. Biol.
, vol.61
, pp. 150-164
-
-
Zhou, X.1
Xu, S.2
Xu, J.3
Chen, B.4
Zhou, K.5
Yang, G.6
-
90
-
-
0036699481
-
Increased taxon sampling greatly reduces phylogenetic error
-
Zwickl D.J., Hillis D.M. 2002. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 51:588-598.
-
(2002)
Syst. Biol.
, vol.51
, pp. 588-598
-
-
Zwickl, D.J.1
Hillis, D.M.2
|