-
1
-
-
0025183708
-
Blast local alignment search tool
-
Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. 1990. Blast local alignment search tool. J. Mol. Biol. 215:403-410.
-
(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
-
2
-
-
26444441397
-
Dating phylogenetically basal eudicots using rbcL sequences and multiple fossil reference points
-
Anderson C.L., Bremer K., Friis E.M. 2005. Dating phylogenetically basal eudicots using rbcL sequences and multiple fossil reference points. Am. J. Bot. 92:1737-1748.
-
(2005)
Am. J. Bot.
, vol.92
, pp. 1737-1748
-
-
Anderson, C.L.1
Bremer, K.2
Friis, E.M.3
-
3
-
-
79957676298
-
Contemporaneous and recent radiations of the world's major succulent plant lineages
-
Arakaki M., Christin P.A., Nyffeler R., Lendel A., Eggli U., Ogburn R.M., Spriggs E., Moore M.J., Edwards E.J. 2011. Contemporaneous and recent radiations of the world's major succulent plant lineages. Proc. Natl Acad. Sci. USA 108:8379-8384.
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 8379-8384
-
-
Arakaki, M.1
Christin, P.A.2
Nyffeler, R.3
Lendel, A.4
Eggli, U.5
Ogburn, R.M.6
Spriggs, E.7
Moore, M.J.8
Edwards, E.J.9
-
4
-
-
84865475040
-
Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty
-
Baele G., Lemey P., Bedford T., Rambaut A., Suchard M.A., Alekseyenko A.V. 2012. Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Mol. Biol. Evol. 29:2157-2167.
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 2157-2167
-
-
Baele, G.1
Lemey, P.2
Bedford, T.3
Rambaut, A.4
Suchard, M.A.5
Alekseyenko, A.V.6
-
5
-
-
77951997517
-
Performance of relaxed-clockmethods in estimating evolutionary divergence times and their credibility intervals
-
Battistuzzi F.U., FilipskiA., Hedges S.B.,Kumar S. 2010. Performance of relaxed-clockmethods in estimating evolutionary divergence times and their credibility intervals. Mol. Biol. Evol. 27:1289-1300.
-
(2010)
Mol. Biol. Evol.
, vol.27
, pp. 1289-1300
-
-
Battistuzzi, F.U.1
Filipski, A.2
Hedges, S.B.3
Kumar, S.4
-
6
-
-
79960016583
-
Convergent Cenozoic CO2 history
-
Beerling D.J., Royer D.L. 2011. Convergent Cenozoic CO2 history. Nat. Geosci. 4:418-420.
-
(2011)
Nat. Geosci.
, vol.4
, pp. 418-420
-
-
Beerling, D.J.1
Royer, D.L.2
-
7
-
-
77955991477
-
The age and diversification of the angiosperms re-revisited
-
Bell C.D., Soltis D.E., Soltis P.S. 2010. The age and diversification of the angiosperms re-revisited. Am. J. Bot. 97:1296-1303.
-
(2010)
Am. J. Bot.
, vol.97
, pp. 1296-1303
-
-
Bell, C.D.1
Soltis, D.E.2
Soltis, P.S.3
-
8
-
-
70149113944
-
The origins and diversification ofC4 grasses and savanna-adaptedungulates
-
Bouchenak-Khelladi Y., Verboom G.A., Hodkinson T.R., Salamin N., Francois O., Chonghaile G.N., Savolainen V. 2009. The origins and diversification ofC4 grasses and savanna-adaptedungulates. Global Change Biol. 15:2397-2417.
-
(2009)
Global Change Biol.
, vol.15
, pp. 2397-2417
-
-
Bouchenak-Khelladi, Y.1
Verboom, G.A.2
Hodkinson, T.R.3
Salamin, N.4
Francois, O.5
Chonghaile, G.N.6
Savolainen, V.7
-
9
-
-
77952787167
-
Biogeography of the grasses (Poaceae): A phylogenetic approach to reveal evolutionary history in geographical space and geological 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 geological time. Bot. J. Linnean Soc. 162:543-557.
-
(2010)
Bot. J. Linnean Soc.
, vol.162
, pp. 543-557
-
-
Bouchenak-Khelladi, Y.1
Verboom, G.A.2
Savolainen, V.3
Hodkinson, T.R.4
-
10
-
-
0036344092
-
Gondwanan evolution of the grass alliance of families (Poales)
-
Bremer K. 2002. Gondwanan evolution of the grass alliance of families (Poales). Evolution 56:1374-1387.
-
(2002)
Evolution
, vol.56
, pp. 1374-1387
-
-
Bremer, K.1
-
11
-
-
34447619825
-
Gondwanan origin of major monocot groups inferred from dispersal-vicariance analysis
-
Bremer K., Jansen T. 2006. Gondwanan origin of major monocot groups inferred from dispersal-vicariance analysis. Aliso 22:22-27.
-
(2006)
Aliso
, vol.22
, pp. 22-27
-
-
Bremer, K.1
Jansen, T.2
-
12
-
-
67650757433
-
TrimAL: A tool for automated alignment trimming in large-scale phylogenetic analyses
-
Capella-Gutierrez S., Silla-Martinez J.M., Gabaldon T. 2009. trimAL: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972-1973.
-
(2009)
Bioinformatics
, vol.25
, pp. 1972-1973
-
-
Capella-Gutierrez, S.1
Silla-Martinez, J.M.2
Gabaldon, T.3
-
13
-
-
33645106540
-
OrthologID: Automation of genome-scale ortholog identification within a parsimony framework
-
Chiu J.C., Lee E.K., Egan M.G., Sarkar I.N., Coruzzi G.M., DeSalle R. 2006. OrthologID: automation of genome-scale ortholog identification within a parsimony framework. Bioinformatics 22:699-707.
-
(2006)
Bioinformatics
, vol.22
, pp. 699-707
-
-
Chiu, J.C.1
Lee, E.K.2
Egan, M.G.3
Sarkar, I.N.4
Coruzzi, G.M.5
Desalle, R.6
-
14
-
-
84888857514
-
The recurrent assembly of C4 photosyn thesis, an evolutionary tale
-
Christin P.A., Osborne C.P. 2013. The recurrent assembly of C4 photosynthesis, an evolutionary tale. Photosynth. Res. 117:163-175.
-
(2013)
Photosynth. Res.
, vol.117
, pp. 163-175
-
-
Christin, P.A.1
Osborne, C.P.2
-
15
-
-
37549037817
-
Oligocene CO2 decline promoted C4 photosynthesis in grasses
-
Christin P.A., Besnard G., Samaritani E., Duvall M.R., Hodkinson T.R., Savolainen V., Salamin N. 2008. Oligocene CO2 decline promoted C4 photosynthesis in grasses. Curr. Biol. 18:37-43.
-
(2008)
Curr. Biol.
, vol.18
, pp. 37-43
-
-
Christin, P.A.1
Besnard, G.2
Samaritani, E.3
Duvall, M.R.4
Hodkinson, T.R.5
Savolainen, V.6
Salamin, N.7
-
16
-
-
79952044347
-
Complex evolutionary transitions and the significance of C3-C4 intermediate forms of photosynthesis in Molluginaceae
-
Christin P.A., Sage T.L., Edwards E.J., Ogburn R.M., Khoshravesh R., Sage R.F. 2011. Complex evolutionary transitions and the significance of C3-C4 intermediate forms of photosynthesis in Molluginaceae. Evolution 65:643-660.
-
(2011)
Evolution
, vol.65
, pp. 643-660
-
-
Christin, P.A.1
Sage, T.L.2
Edwards, E.J.3
Ogburn, R.M.4
Khoshravesh, R.5
Sage, R.F.6
-
17
-
-
84857925836
-
Adaptive evolution of C4 photosynthesis through recurrent lateral gene transfer
-
Christin P.A., Edwards E.J., Besnard G., Boxall S.F., Gregory R.,Kellogg E.A., Hartwell J., Osborne C.P. 2012. Adaptive evolution of C4 photosynthesis through recurrent lateral gene transfer. Curr. Biol. 22:445-449.
-
(2012)
Curr. Biol.
, vol.22
, pp. 445-449
-
-
Christin, P.A.1
Edwards, E.J.2
Besnard, G.3
Boxall, S.F.4
Gregory, R.5
Kellogg, E.A.6
Hartwell, J.7
Osborne, C.P.8
-
18
-
-
77958474295
-
Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution
-
Cibrian-Jaramillo A., De la Torre-Barcena J.E., Lee E.K., Katari M.S., Little D.P., Stevenson D.W., Martienssen R., Coruzzi G.M., DeSalle R. 2010. Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution. Genome Biol. Evol. 2:225-239.
-
(2010)
Genome Biol. Evol.
, vol.2
, pp. 225-239
-
-
Cibrian-Jaramillo, A.1
De La Torre-Barcena, J.E.2
Lee, E.K.3
Katari, M.S.4
Little, D.P.5
Stevenson, D.W.6
Martienssen, R.7
Coruzzi, G.M.8
Desalle, R.9
-
19
-
-
0026281937
-
The earliest remains of grasses in the fossil record
-
CrepetW.L., Feldman G.D. 1991. The earliest remains of grasses in the fossil record. Am. J. Bot. 78:1010-1014.
-
(1991)
Am. J. Bot.
, vol.78
, pp. 1010-1014
-
-
Crepet, W.L.1
Feldman, G.D.2
-
20
-
-
38649110663
-
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
-
22
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar R.C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
23
-
-
84886931475
-
Is it easy to move and easy to evolve? Evolutionary accessibility and adaptation
-
Edwards E.J., Donoghue M.J. 2013. Is it easy to move and easy to evolve? Evolutionary accessibility and adaptation. J. Exp. Bot. 64:4047-4052.
-
(2013)
J. Exp. Bot.
, vol.64
, pp. 4047-4052
-
-
Edwards, E.J.1
Donoghue, M.J.2
-
24
-
-
77951803690
-
The origins of C4 grasslands: Integrating evolutionary and ecosystem science
-
C4 Grasses Consortium
-
Edwards E.J., Osborne C.P., Stromberg C.A.E., Smith S.A., C4 Grasses Consortium. 2010. The origins of C4 grasslands: integrating evolutionary and ecosystem science. Science 328:587-591.
-
(2010)
Science
, vol.328
, pp. 587-591
-
-
Edwards, E.J.1
Osborne, C.P.2
Stromberg, C.A.E.3
Smith, S.A.4
-
25
-
-
0002639864
-
-
Tertiary prairie grasses and other herbs from theHigh Plains
-
Elias M.K. 1942. Tertiary prairie grasses and other herbs from theHigh Plains. Geol. Soc. Am. Special Paper 41:1-176.
-
(1942)
Geol. Soc. Am. Special Paper
, vol.41
, pp. 1-176
-
-
Elias, M.K.1
-
26
-
-
84859548731
-
Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales
-
Faircloth B.C., McCormack J.E., Crawford N.G., Harvey M.G., Brumfield R.T., Glenn T.C. 2012. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst. Biol. 61:717-726.
-
(2012)
Syst. Biol.
, vol.61
, pp. 717-726
-
-
Faircloth, B.C.1
McCormack, J.E.2
Crawford, N.G.3
Harvey, M.G.4
Brumfield, R.T.5
Glenn, T.C.6
-
27
-
-
0141460609
-
Tertiary history of C4 biomass in the Great Plains, USA
-
Fox D.L., Koch P.L. 2003. Tertiary history of C4 biomass in the Great Plains, USA. Geology 31:809-812.
-
(2003)
Geology
, vol.31
, pp. 809-812
-
-
Fox, D.L.1
Koch, P.L.2
-
29
-
-
74049118261
-
Large-scale assignment of orthology: Back to phylogenetics?
-
Gabaldon T. 2008. Large-scale assignment of orthology: back to phylogenetics? Genome Biol. 9:235.
-
(2008)
Genome Biol.
, vol.9
, pp. 235
-
-
Gabaldon, T.1
-
30
-
-
0026469557
-
Relative rates of nucleotide substitution of the rbcL locus of monocotyledonous plants
-
Gaut B.S., Muse S.V., Clark W.D., Clegg M.T. 1992. Relative rates of nucleotide substitution of the rbcL locus of monocotyledonous plants. J. Mol. Evol. 35:292-303.
-
(1992)
J. Mol. Evol.
, vol.35
, pp. 292-303
-
-
Gaut, B.S.1
Muse, S.V.2
Clark, W.D.3
Clegg, M.T.4
-
32
-
-
78650470488
-
Assembling the tree of the Monocotyledons: Plastome sequence phylogeny and evolution of Poale
-
Givnish T.J., Ames M., McNeal J.R., McKain M.R., Steele P.R., dePamphilis C.W., Graham S.W., Pires J.C., Stevenson D.W., Zomlefer W.B., Briggs B.G., Duvall M.R., Moore M.J., Heaney J.M., Soltis D.E., Soltis P.S., Thiele K., Leebens-Mack J.H. 2010. Assembling the tree of the Monocotyledons: plastome sequence phylogeny and evolution of Poales. Ann. MO Bot. Gard. 97:584-616.
-
(2010)
Ann. MO Bot. Gard.
, vol.97
, pp. 584-616
-
-
Givnish, T.J.1
Ames, M.2
McNeal, J.R.3
McKain, M.R.4
Steele, P.R.5
Depamphilis, C.W.6
Graham, S.W.7
Pires, J.C.8
Stevenson, D.W.9
Zomlefer, W.B.10
Briggs, B.G.11
Duvall, M.R.12
Moore, M.J.13
Heaney, J.M.14
Soltis, D.E.15
Soltis, P.S.16
Thiele, K.17
Leebens-Mack, J.H.18
-
33
-
-
0034351387
-
Likelihood-based tests of topologies in phylogenetics
-
GoldmanN., Anderson J.P., Rodrigo A.G. 2000. Likelihood-based tests of topologies in phylogenetics. Syst. Biol. 49:652-670.
-
(2000)
Syst. Biol.
, vol.49
, pp. 652-670
-
-
Goldman, N.1
Anderson, J.P.2
Rodrigo, A.G.3
-
34
-
-
84856585935
-
Phytozome: A comparative platform for green plant genomics
-
Goodstein D.M., Shu S., Howson R., Neupane R., Hayes R.D., Fazo J., Mitros T., Dirks W., Hellsten U., Putnam N., Rokhsar D.S. 2012. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40:D1178-D1186.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Goodstein, D.M.1
Shu, S.2
Howson, R.3
Neupane, R.4
Hayes, R.D.5
Fazo, J.6
Mitros, T.7
Dirks, W.8
Hellsten, U.9
Putnam, N.10
Rokhsar, D.S.11
-
35
-
-
0033666273
-
Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperm
-
Graham S.W., Olmstead R.G. 2000. Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms. Am. J. Bot. 87:1712-1730.
-
(2000)
Am. J. Bot.
, vol.87
, pp. 1712-1730
-
-
Graham, S.W.1
Olmstead, R.G.2
-
36
-
-
84155164309
-
New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins
-
Grass Phylogeny Working Group II
-
Grass Phylogeny Working Group II. 2012. New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins. New Phytol. 193:304-312.
-
(2012)
New Phytol.
, vol.193
, pp. 304-312
-
-
-
37
-
-
0242578620
-
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
-
38
-
-
77649187290
-
Implications of the plastid genome sequence of Typha (Typhaceae, Poales) for understanding genomeevolution inPoaceae
-
Guisinger M.M., Chumley T.W.,Kuehl J.V., Boore J.L., Jansen R.K. 2010. Implications of the plastid genome sequence of Typha (Typhaceae, Poales) for understanding genomeevolution inPoaceae. J. Mol.Evol. 70:149-166.
-
(2010)
J. Mol.Evol.
, vol.70
, pp. 149-166
-
-
Guisinger, M.M.1
Chumley, T.W.2
Kuehl, J.V.3
Boore, J.L.4
Jansen, R.K.5
-
39
-
-
84555188625
-
Calibrated tree priors for relaxed phylogenetics and divergence time estimation
-
Heled J., Drummond A.J. 2012. Calibrated tree priors for relaxed phylogenetics and divergence time estimation. Syst. Biol. 61:138-149.
-
(2012)
Syst. Biol.
, vol.61
, pp. 138-149
-
-
Heled, J.1
Drummond, A.J.2
-
40
-
-
0002211918
-
The fossil history of the monocotyledons
-
Rudall P.J., Cribb P., Cutler D.F.,Umphries C.J., editors Kew, Surrey, UK: Royal Botanic Gardens.
-
Herendeen P.S., Crane P.R. 1995. The fossil history of the monocotyledons. In: Rudall P.J., Cribb P., Cutler D.F.,Umphries C.J., editors. Monocotyledons: systematics and evolution. Kew, Surrey, UK: Royal Botanic Gardens. p. 1-21.
-
(1995)
Monocotyledons: Systematics and Evolution
, pp. 1-21
-
-
Herendeen, P.S.1
Crane, P.R.2
-
41
-
-
67649133122
-
An examination of phylogentic models of substitution rate variation among lineages
-
Ho S.Y.W. 2009. An examination of phylogentic models of substitution rate variation among lineages. Biol. Lett. 5:421-424.
-
(2009)
Biol. Lett.
, vol.5
, pp. 421-424
-
-
Ho, S.Y.W.1
-
42
-
-
70350103638
-
Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times
-
Ho S.Y.W., Phillips M.J. 2009. Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst. Biol. 58:367-380.
-
(2009)
Syst. Biol.
, vol.58
, pp. 367-380
-
-
Ho, S.Y.W.1
Phillips, M.J.2
-
43
-
-
17744387938
-
Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation
-
Ho S.Y.W., Phillips M.J., Drummond A.J., Cooper A. 2005. Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation. Mol. Biol. Evol. 22:1355-1363.
-
(2005)
Mol. Biol. Evol.
, vol.22
, pp. 1355-1363
-
-
Ho, S.Y.W.1
Phillips, M.J.2
Drummond, A.J.3
Cooper, A.4
-
44
-
-
34547762740
-
The impact of fossils and taxon sampling on ancient molecular dating analyses
-
Hug L.A., Roger A.J. 2007. The impact of fossils and taxon sampling on ancient molecular dating analyses. Mol. Biol. Evol. 24:1889-1897.
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 1889-1897
-
-
Hug, L.A.1
Roger, A.J.2
-
45
-
-
0034608819
-
Miocene ungulates and terrestrial primary productivity:Where have all the browsers gone?
-
Janis C.M., Damuth J., Theodor J.M. 2000. Miocene ungulates and terrestrial primary productivity:Where have all the browsers gone? Proc. Natl Acad. Sci. USA 97:7899-7904.
-
(2000)
Proc. Natl Acad. Sci. USA
, vol.97
, pp. 7899-7904
-
-
Janis, C.M.1
Damuth, J.2
Theodor, J.M.3
-
46
-
-
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., Muller K.F., Guisinger-Bellian M., Haberle R.C., Hansen A.K., Chumley T.W., Lee S.B., 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. USA 104:19369-19374.
-
(2007)
Proc. Natl Acad. Sci. USA
, 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
Muller, K.F.7
Guisinger-Bellian, M.8
Haberle, R.C.9
Hansen, A.K.10
Chumley, T.W.11
Lee, S.B.12
Peery, R.13
McNeal, J.R.14
Kuehl, J.V.15
Boore, J.L.16
-
47
-
-
0035103260
-
Performance of a divergence time estimation method under a probabilistic model of rate evolution
-
Kishino J., Thorne J.L., Bruno W.J. 2001. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18:352-361.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 352-361
-
-
Kishino, J.1
Thorne, J.L.2
Bruno, W.J.3
-
48
-
-
33644826560
-
Computing Bayes factors using thermodynamic integration
-
Lartillot N., Philippe H. 2006. Computing Bayes factors using thermodynamic integration. Syst. Biol. 55:195-207.
-
(2006)
Syst. Biol.
, vol.55
, pp. 195-207
-
-
Lartillot, N.1
Philippe, H.2
-
49
-
-
69949126557
-
PhyloBayes 3: A Bayesian software package for phylogenetic reconstruction and molecular dating
-
Lartillot N., Lepage T., Blanquart S. 2009. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25:2286-2288.
-
(2009)
Bioinformatics
, vol.25
, pp. 2286-2288
-
-
Lartillot, N.1
Lepage, T.2
Blanquart, S.3
-
50
-
-
84855272508
-
A functional phylogenomic view of the seed plants
-
Lee E.K., Cibrian-Jaramillo A., Kolokotronis S.O., Katari M.S., Stamastakis A., Ott M., Chiu J.C., Little D.P., Stevenson D.M., McCombie W.R., Martienssen R.A., Coruzzi G., DeSalle R. 2011. A functional phylogenomic view of the seed plants. PLoS Genet. 7:e1002411.
-
(2011)
PLoS Genet.
, vol.7
-
-
Lee, E.K.1
Cibrian-Jaramillo, A.2
Kolokotronis, S.O.3
Katari, M.S.4
Stamastakis, A.5
Ott, M.6
Chiu, J.C.7
Little, D.P.8
Stevenson, D.M.9
McCombie, W.R.10
Martienssen, R.A.11
Coruzzi, G.12
Desalle, R.13
-
51
-
-
24744449757
-
Identifying the basal angiosperm node in chloroplast genome phylogenies: Sampling one's way out of the Feslsenstein zone
-
Leebens-Mack J., Raubeson L.A., Cui L., Kuehl J.V., Fourcade M.H., Chumley T.W., Boore J.L., Jansen R.K., dePamphilis C.W. 2005.Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Feslsenstein zone. Mol. Biol. Evol. 22:1948-1963.
-
(2005)
Mol. Biol. Evol.
, vol.22
, pp. 1948-1963
-
-
Leebens-Mack, J.1
Raubeson, L.A.2
Cui, L.3
Kuehl, J.V.4
Fourcade, M.H.5
Chumley, T.W.6
Boore, J.L.7
Jansen, R.K.8
De Pamphilis, C.W.9
-
52
-
-
84865266483
-
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
-
53
-
-
32044457409
-
Continuous and tractable models for the evolutionary rate
-
Lepage T., Lawi S., Tupper P.F., Bryant D. 2006. Continuous and tractable models for the evolutionary rate. Math. Biosci. 199:216-233.
-
(2006)
Math. Biosci.
, vol.199
, pp. 216-233
-
-
Lepage, T.1
Lawi, S.2
Tupper, P.F.3
Bryant, D.4
-
55
-
-
84555194967
-
Evaluating fossil calibrations for dating phylogenies in light of rates of molecular evolution: A comparison of three approaches
-
Lukoschek V., Keogh J.S., Avise J.C. 2012. Evaluating fossil calibrations for dating phylogenies in light of rates of molecular evolution: a comparison of three approaches. Syst. Biol. 61:22-43.
-
(2012)
Syst. Biol.
, vol.61
, pp. 22-43
-
-
Lukoschek, V.1
Keogh, J.S.2
Avise, J.C.3
-
56
-
-
33644606488
-
Inferring phylogeny despite incomplete lineage sorting
-
Maddison W.P., Knowles L.L. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55:21-30.
-
(2006)
Syst. Biol.
, vol.55
, pp. 21-30
-
-
Maddison, W.P.1
Knowles, L.L.2
-
57
-
-
4944255292
-
Dating lineages: Molecular and paleontological approaches to the temporal framework of clades
-
Magallon S. 2004. Dating lineages: molecular and paleontological approaches to the temporal framework of clades. Int. J. Plant. Sci. 165:S7-S21.
-
(2004)
Int. J. Plant. Sci.
, vol.165
-
-
Magallon, S.1
-
58
-
-
77953773178
-
Using fossils to break long branches in molecular dating: A comparion of relaxed clocks applied to the origin of angiosperms
-
Magallon S. 2010. Using fossils to break long branches in molecular dating: a comparion of relaxed clocks applied to the origin of angiosperms. Syst. Biol. 59:384-399.
-
(2010)
Syst. Biol.
, vol.59
, pp. 384-399
-
-
Magallon, S.1
-
59
-
-
0034765180
-
Absolute diversification rates in angiosperm clades
-
Magallon S., Sanderson M.J. 2001. Absolute diversification rates in angiosperm clades. Evolution 55:1762-1780.
-
(2001)
Evolution
, vol.55
, pp. 1762-1780
-
-
Magallon, S.1
Sanderson, M.J.2
-
60
-
-
84874918225
-
Land plant evolutionary timeline: Gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates
-
Magallon S., Hilu K.W., 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.
-
(2013)
Am. J. Bot.
, vol.100
, pp. 556-573
-
-
Magallon, S.1
Hilu, K.W.2
Quandt, D.3
-
61
-
-
0034931308
-
The breakup history of Gondwana and its impact on pre-Cenozoic floristic provincialism
-
McLoughlin S. 2001. The breakup history of Gondwana and its impact on pre-Cenozoic floristic provincialism. Aust. J. Bot. 49:271-300.
-
(2001)
Aust. J. Bot.
, vol.49
, pp. 271-300
-
-
McLoughlin, S.1
-
62
-
-
22744450037
-
Marked decline in atmospheric carbon dioxide concentrations during the Paleogene
-
Pagani M., Zachos J.C., Freeman K.H., Tipple B., Bohaty S. 2005. Marked decline in atmospheric carbon dioxide concentrations during the Paleogene. Science 309:600-603.
-
(2005)
Science
, vol.309
, pp. 600-603
-
-
Pagani, M.1
Zachos, J.C.2
Freeman, K.H.3
Tipple, B.4
Bohaty, S.5
-
63
-
-
84863116561
-
Best practices for justifying fossil calibrations
-
Parham J.F., Donoghue P.C.J., Bell C.J., Calway T.D., Head J.J., Holroyd P.A., Inoue J.G., Irmis R.B., Joyce W.G., Ksepka D.T., Patane J.S.L., Smith N.D., Tarver J.E., van Tuinen M., Yang Z., Angielczyk K.D., Greenwood J.M., Hipsley C.A., Jacobs L., Makovicky P.J., Muller J., Smith K.T., Theodor J.M., Warnock R.C.M., Benton M.J. 2012. Best practices for justifying fossil calibrations. Syst. Biol. 61:346-359.
-
(2012)
Syst. Biol.
, vol.61
, pp. 346-359
-
-
Parham, J.F.1
Donoghue, P.C.J.2
Bell, C.J.3
Calway, T.D.4
Head, J.J.5
Holroyd, P.A.6
Inoue, J.G.7
Irmis, R.B.8
Joyce, W.G.9
Ksepka, D.T.10
Patane, J.S.L.11
Smith, N.D.12
Tarver, J.E.13
Van Tuinen, M.14
Yang, Z.15
Angielczyk, K.D.16
Greenwood, J.M.17
Hipsley, C.A.18
Jacobs, L.19
Makovicky, P.J.20
Muller, J.21
Smith, K.T.22
Theodor, J.M.23
Warnock, R.C.M.24
Benton, M.J.25
more..
-
65
-
-
27944489518
-
Dinosaur coprolites and the early evolution of grasses and grazers
-
Prasad V., Strömberg C.A.E., Alimohammadian H., Sahni A. 2005. Dinosaur coprolites and the early evolution of grasses and grazers. Science 310:1177-1180.
-
(2005)
Science
, vol.310
, pp. 1177-1180
-
-
Prasad, V.1
Strömberg, C.A.E.2
Alimohammadian, H.3
Sahni, A.4
-
66
-
-
80053395450
-
Late Cretaceous origin of the rice tribe provides evidence for early diversification in Poaceae
-
Prasad V., Strömberg C.A.E., Leaché A.D., Samant B., Patnaik R., Tang L., Mohabey D.M., Ge S., Sahni A. 2011. Late Cretaceous origin of the rice tribe provides evidence for early diversification in Poaceae. Nature Commun. 2:480.
-
(2011)
Nature Commun.
, vol.2
, pp. 480
-
-
Prasad, V.1
Strömberg, C.A.E.2
Leaché, A.D.3
Samant, B.4
Patnaik, R.5
Tang, L.6
Mohabey, D.M.7
Ge, S.8
Sahni, A.9
-
67
-
-
5344230543
-
-
Available from: URL last accessed December 11 2013
-
Rambaut A., Drummond A.J. 2007. Tracer v1.4. Available from: URL http://tree.bio.ed.ac.uk/software/tracer/, (last accessed December 11, 2013).
-
(2007)
Tracer v1.4
-
-
Rambaut, A.1
Drummond, A.J.2
-
68
-
-
14544301560
-
Bayesian molecular dating using PAML/multidivtime
-
Available from: URL
-
Rutschmann F. 2005. Bayesian molecular dating using PAML/multidivtime. A step-by-step manual. Available from: URL ftp://statgen.ncsu.edu/pub/thorne/ bayesiandating1.5.pdf.
-
(2005)
A Step-by-step Manual
-
-
Rutschmann, F.1
-
69
-
-
76749103900
-
Inference of phylogenetic relationships among the subfamilies of grasses (Poaceae: Poales) using mesoscale exemplar-based sampling of the plastid genome
-
Saarela J.M., Graham S.W. 2009. Inference of phylogenetic relationships among the subfamilies of grasses (Poaceae: Poales) using mesoscale exemplar-based sampling of the plastid genome. Botany 88:65-84.
-
(2009)
Botany
, vol.88
, pp. 65-84
-
-
Saarela, J.M.1
Graham, S.W.2
-
70
-
-
77952002714
-
Did gene family expansions during the Eocene-Oligocene boundary climate cooling play a role in Pooideae adaptation to cool climates?
-
Sandve S.R., Fjellheim S. 2010. Did gene family expansions during the Eocene-Oligocene boundary climate cooling play a role in Pooideae adaptation to cool climates? Mol. Ecol. 19:2075-2088.
-
(2010)
Mol. Ecol.
, vol.19
, pp. 2075-2088
-
-
Sandve, S.R.1
Fjellheim, S.2
-
71
-
-
84863116093
-
Testing the impact of calibration on molecular divergence times using a fossil-rich group: The case of Nothofagus (Fagales)
-
Sauquet H., Ho S.Y.W., Gandolfo M.A., Jordan G.J., Wilf P., Cantrill D.J., BaylyM.J., Bromham L., Brown G.K., Carpenter R.J., Lee D.M., Murphy D.J., Sniderman J.M.K., Udovicic F. 2012. Testing the impact of calibration on molecular divergence times using a fossil-rich group: The case of Nothofagus (Fagales). Syst. Biol. 61:289-313.
-
(2012)
Syst. Biol.
, vol.61
, pp. 289-313
-
-
Sauquet, H.1
Ho, S.Y.W.2
Gandolfo, M.A.3
Jordan, G.J.4
Wilf, P.5
Cantrill, D.J.6
Bayly, M.J.7
Bromham, L.8
Brown, G.K.9
Carpenter, R.J.10
Lee, D.M.11
Murphy, D.J.12
Sniderman, J.M.K.13
Udovicic, F.14
-
72
-
-
0032766857
-
Multiple comparisons of loglikelihoods with applications to phylogenetic inference
-
Shimodaira H., Hasegawa M. 1999. Multiple comparisons of loglikelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16:1114-1116.
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 1114-1116
-
-
Shimodaira, H.1
Hasegawa, M.2
-
73
-
-
53349160132
-
Rates of molecular evolution are linked to life history in flowering plants
-
Smith S.A., Donoghue M.J. 2008. Rates of molecular evolution are linked to life history in flowering plants. Science 322:86-89.
-
(2008)
Science
, vol.322
, pp. 86-89
-
-
Smith, S.A.1
Donoghue, M.J.2
-
74
-
-
77950543389
-
An uncorrelated relaxed-clock analysis suggests an earlier origin forflowering plants
-
Smith S.A., Beaulieu J.M., Donoghue M.J. 2010. An uncorrelated relaxed-clock analysis suggests an earlier origin forflowering plants. Proc. Natl Acad. Sci. USA 107:5897-5902.
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 5897-5902
-
-
Smith, S.A.1
Beaulieu, J.M.2
Donoghue, M.J.3
-
75
-
-
78650508629
-
Assembling the angiosperm tree of life: Progress and future prospects
-
Soltis D.E., Moore M.J., Burleigh J.G., Bell C.D., Soltis P.S. 2010. Assembling the angiosperm tree of life: progress and future prospects. Ann. MO Bot. Gard. 97:514-526.
-
(2010)
Ann. MO Bot. Gard.
, vol.97
, pp. 514-526
-
-
Soltis, D.E.1
Moore, M.J.2
Burleigh, J.G.3
Bell, C.D.4
Soltis, P.S.5
-
76
-
-
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.X., 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.X.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..
-
77
-
-
0036889686
-
Orthology, paralogy and proposed classification for paralog subtypes
-
Sonnhammer E.L.L., Koonin E.V. 2002. Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet. 18:619-620.
-
(2002)
Trends Genet.
, vol.18
, pp. 619-620
-
-
Sonnhammer, E.L.L.1
Koonin, E.V.2
-
78
-
-
24744451810
-
Decoupled taxonomic radiation and ecological expansion of open-habitat grasses in the Cenozoic of North America
-
Strömberg C.A.E. 2005. Decoupled taxonomic radiation and ecological expansion of open-habitat grasses in the Cenozoic of North America. Proc. Natl Acad. Sci. USA 102:11980-11984.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 11980-11984
-
-
Strömberg, C.A.E.1
-
79
-
-
0031741182
-
Estimating the rate of evolution of the rate of molecular evolution
-
Thorne J.L., Kishino H., Painter I.S. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15:1647-1657.
-
(1998)
Mol. Biol. Evol.
, vol.15
, pp. 1647-1657
-
-
Thorne, J.L.1
Kishino, H.2
Painter, I.S.3
-
80
-
-
78650090959
-
Isotopic evidence of C4 grasses in southwestern Europe during the early Oligocene-middle Miocene
-
Urban M.A., Nelson D.M., Jimenez-Moreno G., Chateauneuf J.J., Pearson A., Hu F.S. 2010. Isotopic evidence of C4 grasses in southwestern Europe during the early Oligocene-middle Miocene. Geology 38:1091-1094.
-
(2010)
Geology
, vol.38
, pp. 1091-1094
-
-
Urban, M.A.1
Nelson, D.M.2
Jimenez-Moreno, G.3
Chateauneuf, J.J.4
Pearson, A.5
Hu, F.S.6
-
82
-
-
79951566251
-
Improving marginal likelihood estimation for Bayesian phylogenetic model selection
-
XieW., Lewis P.O. Fan Y.Kuo L. Chen M.H. 2011. Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Syst. Biol. 60 150-160.
-
(2011)
Syst. Biol.
, vol.60
, pp. 150-150
-
-
Xie, W.1
Lewis, P.O.2
Fan, Y.3
Kuo, L.4
Chen, M.H.5
-
83
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
Yang Z.H. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24:1586-1591.
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 1586-1591
-
-
Yang, Z.H.1
-
84
-
-
0035957736
-
Trends, rhythms, and aberrations in global climate 60Ma to present
-
Zachos J., Pagani M., Sloan L., Thomas E., Billups K. 2001. Trends, rhythms, and aberrations in global climate 60Ma to present. Science 292:686-693.
-
(2001)
Science
, vol.292
, pp. 686-693
-
-
Zachos, J.1
Pagani, M.2
Sloan, L.3
Thomas, E.4
Billups, K.5
-
85
-
-
38349105013
-
An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics
-
Zachos J.C., Dickens G.R., Zeebe R.E. 2008. An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics. Nature 451:279-283.
-
(2008)
Nature
, vol.451
, pp. 279-283
-
-
Zachos, J.C.1
Dickens, G.R.2
Zeebe, R.E.3
-
86
-
-
65449119576
-
Episodic evolution and adaptation of chloroplast genomes in ancestral grasses
-
Zhong B., Yonezawa T., Zhong Y., Hasegawa M. 2009. Episodic evolution and adaptation of chloroplast genomes in ancestral grasses. PLoS ONE 4:e5297.
-
(2009)
PLoS ONE
, vol.4
-
-
Zhong, B.1
Yonezawa, T.2
Zhong, Y.3
Hasegawa, M.4
-
87
-
-
84866184566
-
Using nuclear gene data for plant phylogenetics: Progress and prospects
-
Zimmer E.A., Wen J. 2012. Using nuclear gene data for plant phylogenetics: progress and prospects. Mol. Phylogenet. Evol. 65:774-785.
-
(2012)
Mol. Phylogenet. Evol.
, vol.65
, pp. 774-785
-
-
Zimmer, E.A.1
Wen, J.2
|