Understanding angiosperm diversification using small and large phylogenetic trees

American Journal of Botany

Volumn 98, Issue 3, 2011, Pages 404-414

  Smith, Stephen A ^a,b   Beaulieu, Jeremy M ^c   Stamatakis, Alexandros ^b   Donoghue, Michael J ^c  

^a BROWN UNIVERSITY   (United States)

^b HEIDELBERG INSTITUTE FOR THEORETICAL STUDIES   (Germany)

^c YALE UNIVERSITY   (United States)

Author keywords

Angiosperms; Diversification rate; Flowering plants; Key innovation; Mega phylogeny

Indexed keywords

DICOTYLEDON; EXTINCTION; GENETIC ANALYSIS; MONOCOTYLEDON; PHYLOGENETICS; PHYLOGENY;

ANGIOSPERM; ARTICLE; BIODIVERSITY; GENETIC VARIABILITY; GENETICS; PHYLOGENY;

ANGIOSPERMS; BIODIVERSITY; GENETIC VARIATION; PHYLOGENY;

ASTERACEAE; FABACEAE; MAGNOLIOPHYTA; ORCHIDACEAE; POACEAE; SPERMATOPHYTA;

EID: 79952762847     PISSN: 00029122     EISSN: None     Source Type: Journal    
DOI: 10.3732/ajb.1000481     Document Type: Article

References (85)

1. Agapow, P., A. Purvis. 2002. Power of eight tree shape statistics to detect non-random diversification: A comparison by simulation of two models of cladogenesis. Systematic Biology 51: 866-872. doi:10.1080/10635150290102564
2. Alfaro, M. E., F. Santini, C. Brock, H. Alamillo, A. Dornburg, D. L. Rabosky, G. Carnevale, L. J. Harmon. 2009. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proceedings of the National Academy of Sciences, USA 106: 13410-13414. doi:10.1073/pnas.0811087106
3. Alvarez, I., J. F. Wendel. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29: 417-434. doi:10.1016/S1055-7903(03)00208-2
4. Angiosperm Phylogeny Group. 2009. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society 161: 105-121.
5. Banks, H., B. B. Klitgaard, F. Claxton, F. Forest, P. R. Crane. 2008. Pollen morphology of the family Polygalaceae (Fabales). Botanical Journal of the Linnean Society 156: 253-289. doi:10.1111/j.1095-8339.2007.00723.x
6. Bell, C. D., D. E. Soltis, P. S. Soltis. 2010. The age and diversification of the angiosperm re-revisited. American Journal of Botany 97: 1296-1303. doi:10.3732/ajb.0900346
7. Bello, M. A., A. Bruneau, F. Forest, J. A. Hawkins. 2009. Elusive relationships within order Fabales: Phylogenetic analyses using matK and rbcL sequence data. Systematic Botany 34: 102-114. doi:10.1600/036364409787602348
8. Bruneau, A., M. Mercure, G. L. Lewis, P. S. Herendeen. 2008. Phylogenetic patterns and diversification in the caesalpinioid legumes. Botany 86: 697-718. doi:10.1139/B08-058
9. Burnham, K. P., D. R. Anderson. [eds.]. 2002. Model selection and multimodel inference: A practical information-theoretic approach. Springer, New York, New York, USA.
10. Cameron, K. M. 2006. A comparison and combination of plastid atpB and rbcL gene sequences for inferring phylogenetic relationships within Orchidaceae. Aliso 22: 447-464.
11. Cantino, P. D., J. A. Doyle, S. W. Graham, W. S. Judd, R. G. Olmstead, D. E. Soltis, P. S. Soltis, M. J. Donoghue. 2007. Toward a phylogentic nomenclature of Tracheophyta. Taxon 56: 822-846. doi:10.2307/25065865
12. Chan, K. M. A., B. R. Moore. 2002. Whole-tree methods for detecting differential diversification rates. Systematic Biology 51: 855-865. doi:10.1080/10635150290102555
13. Chan, K. M. A., B. R. Moore. 2005. SymmeTREE: Whole-tree analysis of differential diversification rates. Bioinformatics (Oxford, England) 21: 1709-1710. doi:10.1093/bioinformatics/bti175
14. Chase, M. W., M. F. Fay, D. Devey, O. Maurin, N. Rønsted, J. Davies, Y. Pillon et al. 2006. Multigene analyses of monocot relationships: A summary. Aliso 22: 63-75.
15. Cooper, A., R. Fortey. 1998. Evolutionary explosions and the phylogenetic fuse. Trends in Ecology & Evolution 13: 151-156. doi:10.1016/S0169-5347(97)01277-9
16. Crane, P. R., E. M. Friis, K. R. Pederson. 1995. The origin and early diversification of angiosperms. Nature 374: 27-33. doi:10.1038/374027a0
17. Crepet, W. L., K. J. Niklas. 2009. Darwin's second abominable mystery: Why are there so many angiosperm species? American Journal of Botany 96: 366-381. doi:10.3732/ajb.0800126
18. Darwin, F., A. C. Seward. [eds.]. 1903. More letters of Charles Darwin. John Murray, London, UK.
19. Davies, T. J., T. G. Barraclough, M. W. Chase, P. S. Soltis, D. E. Soltis, V. Savolainen. 2004. Darwin's abominable mystery: Insights from a supertree of the angiosperms. Proceedings of the National Academy of Sciences, USA 101: 1904-1909. doi:10.1073/pnas.0308127100
20. Davis, J. I., D. W. Stevenson, G. Petersen, O. Seberg, L. M. Campbell, J. V. Freudenstein, D. H. Goldman et al. 2004. A phylogeny of the monocots, as inferred from rbc L and atpA sequence variation, and a comparison of methods for calculating jackknife and bootstrap values. Systematic Botany 29: 467-510. doi:10.1600/0363644041744365
21. De Bodt, S., S. Maere, Y. Van de Peer. 2005. Genome duplication and the origin of angiosperms. Trends in Ecology & Evolution 20: 591-597. doi:10.1016/j.tree.2005.07.008
22. Donoghue, M. J. 2005. Key innovations, convergence, and success: Macroevolutionary lessons from plant phylogeny. Paleobiology 31: 77-93. doi:10.1666/0094-8373(2005)031[0077:KICASM]2.0.CO;2
23. Doyle, J. A. 2001. Significance of molecular phylogenetic analyses for paleobotanical investigations on the origin of angiosperms. Palaeobotanist 50: 167-188.
24. Doyle, J. A., M. J. Donoghue. 1993. Phylogenies and angiosperm diversification. Paleobiology 19: 141-167.
25. Edgar, R. C. 2004. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792-1797. doi:10.1093/nar/gkh340
26. 4 grasses. Proceedings of the National Academy of Sciences, USA 107: 2532-2538. doi:10.1073/pnas.0909672107
27. Endress, P. K., A. Igersheim. 2000. Gynoecium structure and evolution in basal angiosperms. International Journal of Plant Sciences 161, supplement: S211-S223. doi:10.1086/317572
28. Forest, F., A. Bruneau, J. Hawkins, T. Kajita, J. J. Doyle, P. R. Crane. 2002. The sister of the Leguminosae revealed: Phylogenetic relationships in the Fabales determined using trn L and rbcL sequences. In Botany 2002: Botany in the Curriculum, 124, Madison, Wisconsin, USA. Botanical Society of America, St. Louis, Missouri, USA.
29. Friedman, W. E. 2009. The meaning of Darwin's abominable mystery. American Journal of Botany 96: 5-21. doi:10.3732/ajb.0800150
30. Funk, V. A., R. J. Bayer, S. Keeley, R. Chan, L. Watson, B. Gemeinholzer, E. Schilling et al. 2005. Everywhere but Antarctica: Using a supertree to understand the diversity and distribution of the Compositae. Biologiske Skrifter 55: 343-374.
31. Gaut, B. S., S. Muse, W. D. Clark, M. T. Clegg. 1992. Relative rates of nucleotide substitution at the rbcL locus of monocotyledonous plants. Journal of Molecular Evolution 35: 292-303. doi:10.1007/BF00161167
32. Goldberg, E. E., J. R. Kohn, R. Lande, K. A. Robertson, S. A. Smith, B. Igic. 2010. Species selection maintains self-incompatibility. Science 328: 587-591. doi:10.1126/science.1177216
33. Goloboff, P. A. 1999. Analyzing large data sets in reasonable times: Solutions for composite optima. Cladistics 15: 415-428. doi:10.1111/j.1096-0031.1999.tb00278.x
34. Goloboff, P. A., S. A. Catalano, J. M. Mirande, C. A. Szumik, J. S. Arias, M. Källersjö, J. S. Farris. 2009. Phylogenetic analysis of 73060 taxa corroborates major eukaryotic groups. Cladistics 25: 211-230. doi:10.1111/j.1096-0031.2009.00255.x
35. Grass Phylogeny Working Group. 2001. Phylogeny and subfamilial classification of the grasses (Poaceae). Annals of the Missouri Botanical Garden 88: 373-457. doi:10.2307/3298585
36. Guyer, C., J. B. Slowinski. 1993. Adaptive radiation and the topology of large phylogenies. Evolution; International Journal of Organic Evolution 47: 253-263.
37. Hartmann, S., T. Vision. 2008. Can one accurately infer a phylogenetic tree from a gappy alignment? BMC Evolutionary Biology 8: 95. doi:10.1186/1471-2148-8-95
38. Hejnol, A., M. Obst, A. Stamatakis, M. Ott, G. W. Rouse, G. D. Edgecombe, P. Martinez et al. 2009. Assessing the root of bilaterian animals with scalable phylogenomic methods. Proceedings. Biological Sciences 276: 4261-4270. doi:10.1098/rspb.2009.0896
39. Holman, E. W. 2005. Nodes in phylogenetic trees: The relation between imbalance and number of descendent species. Systematic Biology 54: 895-899. doi:10.1080/10635150500354696
40. Jansen, R. K., Z. Cai, L. A. Raubeson, H. Daniell, C. W. dePamphilis, J. Leebens-Mack, K. F. Müller et al. 2007. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proceedings of the National Academy of Sciences, USA 104: 19369-19374. doi:10.1073/pnas.0709121104
41. Katoh, K., H. Toh. 2008. Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics 9: 286-298. doi:10.1093/bib/bbn013
42. Leebens-Mack, J., L. A. Raubeson, L. Cui, J. V. Kuehl, M. H. Fourcade, T. W. Chumley, J. L. Boore, R. K. Jansen, C. W. dePamphilis. 2005. Identifying the basal angiosperm node in chloroplast genome phylogenies: Sampling one's way out of the Felsenstein zone. Molecular Biology and Evolution 22: 1948-1963. doi:10.1093/molbev/msi191
43. Lemmon, A. R., J. M. Brown, K. Stanger-Hall, E. M. Lemmon. 2009. The effect of missing data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Systematic Biology 58: 130-145. doi:10.1093/sysbio/syp017
44. Liow, L. H., T. B. Quental, C. R. Marshall. 2010. When can decreasing diversification rates be detected with molecular phylogenies and the fossil record? Systematic Biology 59: 646-659. doi:10.1093/sysbio/syq052
45. Magallón, S. 2010. Using fossils to break long branches in molecular dating: A comparison of relaxed clocks applied to the origin of angiosperms. Systematic Biology 59: 384-399. doi:10.1093/sysbio/syq027
46. Magallón, S., M. J. Sanderson. 2001. Absolute diversification rates in angiosperm clades. Evolution; International Journal of Organic Evolution 55: 1762-1780.
47. McMahon, M. M., M. J. Sanderson. 2006. Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes. Systematic Biology 55: 818-836. doi:10.1080/10635150600999150
48. Mooers, A. O., S. B. Heard. 1997. Inferring evolutionary process from the phylogenetic tree shape. The Quarterly Review of Biology 72: 31-54. doi:10.1086/419657
49. Moore, B. R., K. M. A. Chan, M. J. Donoghue. 2004. Detecting diversification rate variation in supertrees. In O. R. P. Bininda-Emonds [ed.], Phylogenetic supertrees: Combining information to reveal the tree of life, 487-533. Kluwer, Dordrecht, Netherlands.
50. Moore, M. J., C. D. Bell, P. S. Soltis, D. E. Soltis. 2007. Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms. Proceedings of the National Academy of Sciences, USA 104: 19363-19368. doi:10.1073/pnas.0708072104
51. Moore, B. R., M. J. Donoghue. 2007. Correlates of diversification in the plant clade Dipsacales: Geographic movement and evolutionary innovations. American Naturalist 170: S28-S55. doi:10.1086/519460
52. Moore, B. A., M. J. Donoghue. 2009. A Bayesian approach for evaluating the impact of historical events on rates of diversification. Proceedings of the National Academy of Sciences, USA 106: 4307-4312. doi:10.1073/pnas.0807230106
53. Nee, S. 2001. Inferring speciation rates from phylogenies. Evolution; International Journal of Organic Evolution 55: 661-668.
54. Nee, S., A. Mooers, P. H. Harvey. 1992. Tempo and mode of evolution revealed from molecular phylogenies. Proceedings of the National Academy of Sciences, USA 89: 8322-8326. doi:10.1073/pnas.89.17.8322
55. Panero, J. L., V. A. Funk. 2002. Toward a phylogenetic classification for the Compositae (Asteraceae). Proceedings of the Biological Society of Washington 115: 909-922.
56. Panero, J. L., V. A. Funk. 2008. The value of sampling anomalous taxa in phylogenetic studies: Major clades of the Asteraceae revisited. Molecular Phylogenetics and Evolution 47: 757-782. doi:10.1016/j.ympev.2008.02.011
57. Purvis, A., A. Katzourakis, P. Agapow. 2002. Evaluating phylogenetic tree shape: Two modifications to Fusco and Cronk's method. Journal of Theoretical Biology 214: 99-103. doi:10.1006/jtbi.2001.2443
58. Qiu, Y., L. Li, B. Wang, Z. Chen, V. Knoop, M. Groth-Malonek, O. Dombrovska et al. 2006. The deepest divergences in land plants inferred from phylogenomic evidence. Proceedings of the National Academy of Sciences, USA 103: 15511-15516. doi:10.1073/pnas.0603335103
59. Rabosky, D. L. 2009. Extinction rates should not be estimated from molecular phylogenies. Evolution; International Journal of Organic Evolution 64: 1816-1824.
60. Rabosky, D. L., I. J. Lovette. 2008. Density-dependent diversification in North American wood warblers. Proceedings of the Royal Society of London. Series B. Biological Sciences 275: 2363-2371.
61. Raikow, R. J. 1986. Why are there so many kinds of passerine birds? Systematic Zoology 35: 255-259. doi:10.2307/2413436
62. Ramírez, S. R., B. Gravendeel, R. B. Singer, C. R. Marshall, N. E. Pierce. 2007. Dating the origin of Orchidaceae from a fossil orchid with its pollinator. Nature 448: 1042-1045. doi:10.1038/nature06039
63. Ricklefs, R. E. 2007. Estimating diversification rates from phylogenetic information. Trends in Ecology & Evolution 22: 601-610. doi:10.1016/j.tree.2007.06.013
64. Sanderson, M. J., M. J. Donoghue. 1994. Shifts in diversification rate with the origin of angiosperms. Science 264: 1590-1593. doi:10.1126/science.264.5165.1590
65. Sanderson, M. J., M. J. Donoghue. 1996. Reconstructing shifts in diversification on phylogenetic trees. Trends in Ecology & Evolution 11: 15-20. doi:10.1016/0169-5347(96)81059-7
66. Sanderson, M. J., M. M. McMahon, M. Steel. 2010. Phylogenomics with incomplete taxon coverage: the limits to inference. BMC Evolutionary Biology 10: 155. doi:10.1186/1471-2148-10-155
67. Santini, F., L. J. Harmon, G. Carnevale, M. Alfaro. 2009. Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes. BMC Evolutionary Biology 9: 194. doi:10.1186/1471-2148-9-194
68. Scotland, R. W., A. H. Wortley. 2003. How many species of seed plant are there? Taxon 52: 101-104. doi:10.2307/3647306
69. Slowinski, J. B., C. Guyer. 1989. Testing the stochasticity of patterns of organismal diversity: An improved null model. American Naturalist 134: 907-921. doi:10.1086/285021
70. Smith, S. A., J. M. Beaulieu. 2009. Life history influences rates of climatic niche evolution in flowering plants. Proceedings of the Royal Society of London. Series B. Biological Sciences 276: 4345-4352. doi:10.1098/rspb.2009.1176
71. Smith, S. A., J. M. Beaulieu, M. J. Donoghue. 2009. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evolutionary Biology 9: 37. doi:10.1186/1471-2148-9-37
72. Smith, S. A., J. M. Beaulieu, M. J. Donoghue. 2010. An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants. Proceedings of the National Academy of Sciences, USA 107: 5897-5902. doi:10.1073/pnas.1001225107
73. Smith, S. A., M. J. Donoghue. 2008. Rates of molecular evolution are linked to life history in flowering plants. Science 322: 86-89.
74. Soltis, D. E., A. S. Chanderbali, S. Kim, M. Buzgo, P. S. Soltis. 2007. The ABC model its applicability to basal angiosperms. American Journal of Botany 100: 155-163. doi:10.1093/aob/mcm117
75. Soltis, D. E., S. A. Smith, N. Cellinese, M. J. Moore, C. C. Davis, K. J. Wurdack, S. F. Brockington et al. In press. Inferring angiosperm phylogeny: 17 gene analyses. American Journal of Botany.
76. Stamatakis, A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (Oxford, England) 22: 2688-2690. doi:10.1093/bioinformatics/btl446
77. Stamatakis, A., P. Hoover, J. Rougemont. 2008. A rapid bootstrap algorithm for the RaxML web servers. Systematic Biology 57: 758-771. doi:10.1080/10635150802429642
78. Stevens, P. F. 2010. Angiosperm Phylogeny Website, version 9, June 2008 [and more or less continuously updated since]. Website http://www.mobot.org/MOBOT/research/APweb/.
79. Thomson, R. C., H. B. Shaffer. 2010. Rapid progress on the vertebrate tree of life. BMC Biology 8: 19. doi:10.1186/1741-7007-8-19
80. Wertheim, J. O., M. J. Sanderson. 2010. Estimating diversification rates: how useful are divergence times? Evolution; International Journal of Organic Evolution 65: 309-320.
81. Wiens, J. J. 2003. Missing data, incomplete taxa, phylogenetic accuracy. Systematic Biology 52: 528-538. doi:10.1080/10635150390218330
82. Wiens, J. J. 2005. Can incomplete taxa rescue phylogenetic analyses from long-branch attraction? Systematic Biology 54: 731-742. doi:10.1080/10635150500234583
83. Wojciechowski, M. F., M. Lavin, M. J. Sanderson. 2004. A phylogeny of legumes (Leguminosae) based on analysis of the plastid matK gene resolves many well-supported subclades within the family. American Journal of Botany 91: 1846-1862. doi:10.3732/ajb.91.11.1846
84. Worberg, A., D. Quandt, A. M. Barniske, C. Löhne, K. W. Hilu, T. Borsch. 2007. Phylogeny of basal eudicots: Insights from non-coding and rapidly evolving DNA. Organisms, Diversity & Evolution 7: 55-77. doi:10.1016/j.ode.2006.08.001
85. Zwickl, D. J. 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. dissertation, University of Texas at Austin, Austin, Texas, USA.