Phylogeny and Phylogenetic Nomenclature of the Campanulidae Based on an Expanded Sample of Genes and Taxa

Systematic Botany

Volumn 35, Issue 2, 2010, Pages 425-441

  Tank, David C ^a,b   Donoghue, Michael J ^a  

^a YALE UNIVERSITY   (United States)

^b UNIVERSITY OF IDAHO   (United States)

Author keywords

angiosperm phylogeny; Asteridae; Campanulidae; Euasterid II; phylogenetic nomenclature

Indexed keywords

APIALES; ASTERALES; ASTERIDS; BRUNIACEAE; COLUMELLIACEAE; DIPSACALES; ESCALLONIACEAE; MAGNOLIOPHYTA;

EID: 77954488234     PISSN: 03636445     EISSN: 15482324     Source Type: Journal    
DOI: 10.1600/036364410791638306     Document Type: Article

References (89)

1. Albach, D. C., P. S. Soltis, D. E. Soltis, and R. G. Olmstead. 2001. Phylogenetic analysis of asterids based on sequences of four genes. Annals of the Missouri Botanical Garden 88:163-212.
2. Alfaro, M. E., S. Zoller, and F. Lutzoni. 2003. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Molecular Biology and Evolution 20:255-266.
3. Anderberg, A. A., B. G. Baldwin, R. G. Bayer, J. Breitwieser, C. Jeffrey, M. O. Dillon, P. Eldenäs, V. Funk, N. Garcia-Jacas, D. J. N. Hind, P. O. Karis, H. W. Lack, G. Nesom, B. Nordenstam, Ch. Oberprieler, J. L. Panero, C. Puttock, H. Robinson, T. F. Stuessy, A. Susanna, E. Urtubey, R. Vogt, J. Ward, and L. E. Watson. 2007. Compositae. Pp. 61-588 in The families and genera of vascular plants vol. 8, eds. J. W. Kadereit and C. Jeffrey. Berlin: Springer Verlag.
4. APG (Angiosperm Phylogeny Group). 1998. An ordinal classification for the families of flowering plants. Annals of the Missouri Botanical Garden 85:531-553.
5. APG (Angiosperm Phylogeny Group) II. 2003. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Botanical Journal of the Linnean Society 141:399-436.
6. Armbruster, W. S. and N. Muchhala. 2009. Associations between floral specialization and species diversity: cause, effect, or correlation? Evolutionary Ecology 23:159-179.
7. Bell, C. B. and M. J. Donoghue. 2003. Phylogeny of Morinaceae (Dipsacales) based on nuclear and chloroplast DNA sequences. Organisms, Evolution, and Diversity 3:227-237.
8. Brandley, M. C., A. Schmitz, and T. W. Reeder. 2005. Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Systematic Biology 54:373-390.
9. Bremer, B., K. Bremer, N. Heidari, P. Erixon, R. G. Olmstead, A. A. Anderberg, M. Källersjö, and E. Barkhordarian. 2002. Phylogenetics of asterids based on 3 coding and 3 non-coding chloroplast DNA markers and the utility of non-coding DNA at higher taxonomic levels. Molecular Phylogenetics and Evolution 24:274-301.
10. Bremer, K. 1994. Asteraceae: cladistics and classification. Portland: Timber Press.
11. Bult, C. J., M. Källersjö, and Y. Suh. 1992. Amplification and sequencing of 16/18S rDNA from gel-purified total plant DNA. Plant Molecular Biology Reporter 10:273-284.
12. Cantino, P. D. and K. de Queiroz. 2007. PhyloCode: a phylogenetic code of biological nomenclature. Version 4b. Website: http://www.phylocode.org. Revised September 12, 2007.
13. Cantino, P. D., J. A. Doyle, S. W. Graham, W. S. Judd, R. G. Olmstead, P. S. Soltis, D. E. Soltis, and M. J. Donoghue. 2007. Towards a phylogenetic nomenclature of Tracheophyta. Taxon 56:822-846.
14. Carlson, S. E., V. Mayer, and M. J. Donoghue. 2009. Phylogenetic relationships, taxonomy, and morphological evolution in Dipsacaceae (Dipsacales) inferred by DNA sequence data. Taxon 58:1075-1091.
15. Chandler, G. T. and G. M. Plunkett. 2004. Evolution in Apiales: nuclear and chloroplast markers together in (almost) perfect harmony. Botanical Journal of the Linnean Society 144:123-147.
16. Chase, M. W., D. E. Soltis, R. G. Olmstead, D. Morgan, D. H. Les, B. D. Mishler, M. R. Duvall, R. A. Price, H. G. Hills, Y.-L. Qiu, K. A. Kron, J. H. Rettig, E. Conti, J. D. Palmer, J. R. Manhart, K. J. Sytsma, H. J. Michaels, W. J. Kress, K. G. Karol, W. D. Clark, M. Hedren, B. S. Gaut, R. K. Jansen, K. J. Kim, C. F. Wimpee, J. F. Smith, G. R. Furnier, S. H. Strauss, Q.-Y. Xiang, G. M. Plunkett, P. S. Soltis, S. M. Swensen, S. E. Williams, P. A. Gadek, C. J. Quinn, L. E. Eguiarte, E. Golenberg, G. H. Learn, S. W. Graham, S. C. H. Barrett, S. Dayanandan, and V. A. Albert. 1993. Phylogenetics of seed plants - an analysis of nucleotidesequences from the plastid gene rbcL. Annals of the Missouri Botanical Garden 80:528-580.
17. Cronquist, A. 1981. An integrated system of classification of flowering plants. New York: Columbia University Press.
18. Cummings, M. P., S. A. Handley, D. S. Myers, D. L. Reed, A. Rokas, and K. Winka. 2003. Comparing bootstrap and posterior probability values in the four-taxon case. Systematic Biology 52:477-487.
19. Davis, C. C., C. O. Webb, K. J. Wurdack, C. A. Jaramillo, and M. J. Donoghue. 2005. Explosive radiation of Malpighiales supports a mid-Cretaceous origin of modern tropical rain forests. American Naturalist 165: E36-E65.
20. de Queiroz, K. 1992. Phylogenetic definitions and taxonomic philosophy. Biology and Philosophy 7:295-313.
21. de Queiroz, K. and J. Gauthier. 1990. Phylogeny as a central principle in taxonomy: phylogenetic definitions of taxon names. Systematic Zoology 39:307-322.
22. de Queiroz, K. and J. Gauthier. 1992. Phylogenetic taxonomy. Annual Review of Ecology and Systematics 23:449-480.
23. de Queiroz, K. and J. Gauthier. 1994. Toward a phylogenetic system of biological nomenclature. Trends in Ecology & Evolution 9:27-31.
24. Delwiche, C. F., R. A. Anderson, D. Bhattacharya, B. D. Mishler, and R. M. McCourt. 2004. Algal evolution and the early radiation of green plants. Pp. 121-137 in Assembling the tree of life, eds. J. Cracraft and M. J. Donoghue. New York: Oxford University Press.
25. Donoghue, M. J. 2004. Immeasurable progress on the tree of life. Pp. 548-552 in Assembling the tree of life, eds. J. Cracraft and M. J. Donoghue. New York: Oxford University Press.
26. Donoghue, M. J., C. D. Bell, and R. C. Winkworth. 2003. The evolution of reproductive characters in Dipsacales. International Journal of Plant Sciences 164: S453-S464.
27. Donoghue, M. J., T. Eriksson, P. A. Reeves, and R. G. Olmstead. 2001. Phylogeny and phylogenetic taxonomy of Dipsacales, with special reference to Sinadoxa and Tetradoxa (Adoxaceae). Harvard Papers in Botany 6:459-479.
28. Doyle, J. J. and J. L. Doyle. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19:11-15.
29. Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32:1792-1797.
30. Erixon, P., B. Svennblad, T. Britton, and B. Oxelman. 2003. Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Systematic Biology 52:665-673.
31. Graham, S. W. and W. J. D. Iles. 2009. Different gymnosperm outgroups have (mostly) congruent signal regarding the root of flowering plant phylogeny. American Journal of Botany 96:216-227.
32. Graham, S. W. and R. G. Olmstead. 2000. Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms. American Journal of Botany 87:1712-1730.
33. Gustafsson, M. H. G. 1996. Phylogenetic studies in the Asterales sensu lato. Doctoral Dissertation. Uppsala, Sweden: Uppsala University.
34. Gustafsson, M. H. G., A. S. R. Pepper, V. A. Albert, and M. Källersjö. 2001. Molecular phylogeny of the Barnadesioideae (Asteraceae). Nordic Journal of Botany 21:149-160.
35. Hara, H. 1983. A revision of the Caprifoliaceae of Japan with reference to allied plants in other districts and the Adoxaceae. Tokyo: Academia Scientific Books.
36. Hillis, D. M. 1996. Inferring complex phylogenies. Nature 383:130-131.
37. Hillis, D. M. 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Systematic Biology 47:3-8.
38. Hoot, S. B., A. Culham, and P. R. Crane. 1995. The utility of atpB gene sequences in resolving phylogenetic relationships: comparison with rbcL and 18S ribosomal DNA-sequences in the Lardizabalaceae. Annals of the Missouri Botanical Garden 82:194-207.
39. Howarth, D. G. and M. J. Donoghue. 2005. Duplications in the CYC-like genes of Dipsacales correlate with floral form. International Journal of Plant Sciences 166:357-370.
40. Howarth, D. G. and M. J. Donoghue. 2009. Duplications and expression of DIVARICATA-like genes in Dipsacales. Molecular Biology and Evolution 26:1245-1258.
41. Jansen, R. K., Z. Cai, L. A. Raubeson, H. Daniell, C. W. de Pamphilis, J. Leebens-Mack, K. F. Mueller, M. Guisinger-Bellian, R. C. Haberle, A. K. Hansen, T. W. Chumley, S. Lee, R. Peery, J. R. McNeal, J. V. Kuehl, and J. L. Boore. 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.
42. Jeffrey, C. 1977. Corolla forms in Compositae - some evolutionary and taxonomic speculations. Pp. 111-118 in The biology and chemistry of the Compositae, vol. 1, eds. V. H. Heywood, J. B. Harborne, and B. L. Turner. London: Academic Press.
43. Jian, S., P. S. Soltis, M. Gitzendanner, M. J. Moore, R. Li, T. Hendry, Y.-L. Qiu, A. Dhingra, C. Bell, and D. E. Soltis. 2008. Resolving an ancient, rapid radiation in Saxifragales. Systematic Biology 57:1-20.
44. Judd, W. S. and R. G. Olmstead. 2004. Asurvey of tricolpate (eudicot) phylogenetic relationships. American Journal of Botany 91:1627-1644.
45. Kårehed, J. 2001. Multiple origin of the tropical forest tree family Icacinaceae. American Journal of Botany 88:2259-2274.
46. Kårehed, J. 2002. Evolutionary studies in Asterids emphasising Euasterids II. Doctoral Dissertation. Uppsala, Sweden: Uppsala University.
47. Kårehed, J. 2003. The family Pennantiaceae and its relationships to Apiales. Botanical Journal of the Linnean Society 141:1-24.
48. Kuzoff, R. K., J. A. Sweere, D. E. Soltis, P. S. Soltis, and E. A. Zimmer. 1998. The phylogenetic potential of entire 26S rDNA sequences in plants. Molecular Biology and Evolution 15:251-263.
49. Laurent, N., B. Bremer, and K. Bremer. 1999. Phylogeny and generic interrelationships of the Stylidiaceae (Asterales), with a possible extreme case of floral paedomorphosis. Systematic Botany 23:289-304.
50. Lammers, T. G. 2007. Campanulaceae. Pages 26-56 in The families and genera of vascular plants vol. 8, eds. J. W. Kadereit and C. Jeffrey. Berlin: Springer Verlag.
51. Lundberg, J. 2001. Phylogenetic studies in the Euasterids II with particular reference to Asterales and Escalloniaceae. Doctoral Dissertation. Uppsala, Sweden: Uppsala University.
52. Lundberg, J. and K. Bremer. 2003. A phylogenetic study of the order Asterales using one morphological and three molecular data sets. International Journal of Plant Sciences 164:553-578.
53. Magallón, S. and A. Castillo. 2009. Angiosperm diversification through time. American Journal of Botany 96:349-365.
54. Moore, B. R. and M. J. Donoghue. 2007. Correlates of diversification in the plant clade Dipsacales: Geographic movement and evolutionary innovations. American Naturalist 170: S28-S55.
55. Moore, B. R., S. A. Smith, and M. J. Donoghue. 2006. Increasing data transparency and estimating phylogenetic uncertainty in supertrees: approaches using nonparametric bootstrapping. Systematic Biology 55:662-676.
56. Moore, M. J., C. D. Bell, P. S. Soltis, and 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.
57. Morgan, D. R. and D. E. Soltis. 1993. Phylogenetic relationships among members of Saxifragaceae sensu lato based on rbcL sequence data. Annals of the Missouri Botanical Garden 80:631-660.
58. Olmstead, R. G., K. J. Kim, R. K. Jansen, and S. J. Wagstaff. 2000. The phylogeny of the Asteridae sensu lato based on chloroplast ndhF gene sequences. Molecular Phylogenetics and Evolution 16:96-112.
59. Olmstead, R. G. and P. A. Reeves. 1995. Evidence for the polyphyly of the Scrophulariaceae based on chloroplast rbcL and ndhF sequences. Annals of the Missouri Botanical Garden 82:176-193.
60. Olmstead, R. G. and J. A. Sweere. 1994. Combining data in phylogenetic systematics - an empirical approach using 3 molecular data sets in the Solanaceae. Systematic Biology 43:467-481.
61. Oxelman, B., M. Liden, and D. Berglund. 1997. Chloroplast rps16 intron phylogeny of the tribe Sileneae (Caryophyllaceae). Plant Systematics and Evolution 206:393-410.
62. Panero, J. L. and V. A. Funk. 2008. The value of sampling anomalous taxa in phylogenetic studies: major clades of the Asteraceae revealed. Molecular Phylogenetics and Evolution 47:757-782.
63. Posada, D. and K. A. Crandall. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818.
64. Pryer, K. M., H. Schneider, and S. Magallón. 2004. The radiation of vascular plants. Pp. 138-153 in Assembling the tree of life, eds. J. Cracraft and M. J. Donoghue. New York: Oxford University Press.
65. Qiu, Y.-L., O. Dombrovska, J. Lee, L.-B. Li, B. A. Whitlock, F. Bernasconi-Quadroni, J. S. Rest, C. C. Davis, T. Borsch, K. W. Hilu, S. S. Renner, D. E. Soltis, P. S. Soltis, M. J. Zanis, J. J. Cannone, R. R. Gutell, M. Powell, V. Savolainen, L. W. Chatrou, and M. W. Chase. 2005. Phylogenetic analyses of basal angiosperms based on nine plastid, mitochondrial, and nuclear genes. International Journal of Plant Sciences 166:815-842.
66. Rambaut, A. 1996. Se-Al: Sequence Alignment Editor. Available at http://tree. bio.ed.ac.uk/software/seal/. Edinburgh: University of Edinburgh.
67. Rambaut, A. and A. J. Drummond. 2004. Tracer. Available at http://tree. bio.ed.ac.uk/software/tracer/. Edinburgh: University of Edinburgh.
68. Ronquist, F. and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
69. Sang, T., D. J. Crawford, and T. F. Stuessy. 1997. Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). American Journal of Botany 84:1120-1136.
70. Simmons, M. P., K. M. Pickett, and M. Miya. 2004. How meaningful are Bayesian support values? Molecular Biology and Evolution 21:188-199.
71. Smith, S. A. and M. J. Donoghue. 2008. Rates of molecular evolution are linked to life history in flowering plants Science. Science 322:86-89.
72. Smith, S. A. and C. Dunn. 2008. Phyutility: a phyloinformatics utility for trees, alignments, and molecular data. Bioinformatics 24:715-716.
73. Smith, S. A., J. M. Beaulieu, and M. J. Donoghue. 2009. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evolutionary Biology 9:37.
74. Soltis, D. E., M. A. Gitzendanner, and P. S. Soltis. 2007. A567-taxon data set for angiosperms: The challenges posed by bayesian analyses of large data sets. International Journal of Plant Sciences 168:137-157.
75. Soltis, D. E. and P. S. Soltis. 1997. Phylogenetic relationships in Saxifragaceae sensu lato: A comparison of topologies based on 18S rDNA and rbcL sequences. American Journal of Botany 84:504-522.
76. Soltis, D. E., P. S. Soltis, M. W. Chase, M. E. Mort, D. C. Albach, M. Zanis, V. Savolainen, W. H. Hahn, S. B. Hoot, M. F. Fay, M. Axtell, S. M. Swensen, L. M. Prince, W. J. Kress, K. C. Nixon, and J. S. Farris. 2000. Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences. Botanical Journal of the Linnean Society 133:381-461.
77. Soltis, P. S., D. E. Soltis, M. W. Chase, P. K. Endress, and P. R. Crane. 2004. The diversification of flowering plants. Pp. 154-170 in Assembling the tree of life, eds. J. Cracraft and M. J. Donoghue. New York: Oxford University Press.
78. Stamatakis, A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
79. Stamatakis, A., P. Hoover, and J. Rougemont. 2008. Arapid bootstrap algorithm for the RAxML web servers. Systematic Biology 57:758-771.
80. Stevens, P. F. (2001 onwards). Angiosperm Phylogeny Website. http://www.mobot.org/MOBOT/research/APweb/. St. Louis: Missouri Botanical Garden.
81. Suzuki, Y., G. V. Glazko, and M. Nei. 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proceedings of the National Academy of Sciences USA 99:16138-16143.
82. Taberlet, P., L. Gielly, G. Pautou, and J. Bouvet. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17:1105-1109.
83. Urtubey, E. and T. F. Stuessy. 2001. New hypotheses of phylogenetic relationships in Barnadesioideae (Asteraceae) based on morphology. Taxon 50:1043-1066.
84. Wagstaff, S. J. and J. Wege. 2002. Patternsof diversificationin New Zealand Stylidiaceae. American Journal of Botany 89:865-874.
85. Wang, H., M. J. Moore, P. S. Soltis, C. D. Bell, S. F. Brockington, R. Alexandre, C. C. Davis, M. Latvis, S. R. Manchester, and D. E. Soltis. 2009. Rosid radiation and the rapid rise of angiosperm-dominated forests. Proceedings of the National Academy of Sciences USA 106:3853-3858.
86. Winkworth, R. C., C. D. Bell, and M. J. Donoghue. 2008a. Mitochondrial sequence data and Dipsacales phylogeny: Mixed models, partitioned Bayesian analyses, and model selection. Molecular Phylogenetics and Evolution 46:830-843.
87. Winkworth, R. C., J. Lundberg, and M. J. Donoghue. 2008b. Toward a resolution of campanulid phylogeny, with a special reference to the placement of Dipsacales. Taxon 57:53-65.
88. Wilcox, T. P., D. J. Zwickl, T. A. Heath, and D. M. Hillis. 2002. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Molecular Phylogenetics and Evolution 25:361-371.
89. Zwickl, D. J. and D. M. Hillis. 2002. Increased taxon sampling greatly reduces phylogenetic error. Systematic Biology 51:588-598.