Phylogeny of celastraceae subfamilies cassinoideae and tripterygioideae inferred from morphological characters and nuclear and plastid loci

Systematic Botany

Volumn 37, Issue 2, 2012, Pages 456-467

  Simmons, Mark P ^a   Bacon, Christine D ^a   Cappa, Jennifer J ^a   McKenna, Miles J ^a  

^a Department of Environmental and Radiological Health Sciences   (United States)

Author keywords

Acanthothamnus; Canotia; Orthosphenia; Rzedowskia; Siphonodon; Zinowiewia

Indexed keywords

ACANTHOTHAMNUS; CANOTIA; CELASTRACEAE; CROSSOPETALUM; GYMINDA; MAYTENUS; ORTHOSPHENIA; PLEUROSTYLIA; RZEDOWSKIA; SCHAEFFERIA (ANGIOSPERM); SIPHONODON; TRIPTERYGIUM; WIMMERIA; ZINOWIEWIA;

EID: 84860811512     PISSN: 03636445     EISSN: 15482324     Source Type: Journal    
DOI: 10.1600/036364412X635502     Document Type: Article

References (110)

1. Adams, C. D. 1972. Flowering plants of Jamaica. Mona: University of the West Indies.
2. Airy Shaw, H. K., D. F. Cutler, and S. Nilsson. 1973. Pottingeria, its taxonomic position, anatomy and palynology. Kew Bulletin 28: 97-104.
3. Akaike, H. 1974. A new look at the statistical model identification. IEEE Transactions on Automatic Control 19: 716-723.
4. Alexander, P. J., G. Rajanikanth, C. D. Bacon, and C. D. Bailey. 2006. Recovery of plant DNA using a reciprocating saw and silica-based columns. Molecular Ecology Notes 7: 5-9. (Pubitemid 46046570)
5. Álvarez, I. and J. F. Wendel. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29: 417-434. (Pubitemid 37491888)
6. Archer, R. H. and A. E. van Wyk. 1997. A taxonomic revision of Cassine L. s. str. (Cassinoideae: Celastraceae). South African Journal of Botany 63: 146-157. (Pubitemid 27344293)
7. Archer, R. H. and A. E. van Wyk. 1998. A taxonomic revision of Maurocenia (Celastraceae), a Western Cape monotypic endemic. Bothalia 28: 7-10. (Pubitemid 29053260)
8. Bailey, C. D., T. G. Carr, S. A. Harris, and C. E. Hughes. 2003. Characterization of angiosperm nrDNA polymorphism, paralogy, and pseudogenes. Molecular Phylogenetics and Evolution 29: 435-455. (Pubitemid 37491889)
9. Bailey, L. H., E. Z. Bailey, and Staff of the Liberty Hyde Bailey Hortorium. 1976. Hortus third: a concise dictionary of plants cultivated in the United States and Canada. New York: MacMillan Publishing Co., Inc.
10. Bensel, C. R. and B. F. Palser. 1975. Floral anatomy in the Saxifragaceae s. l. I. Introduction, Parnassioideae and Brexioideae. American Journal of Botany 62: 176-185.
11. Blattner, F. R. 1999. Direct amplification of the entire ITS region from poorly preserved plant material using recombinant PCR. Bio- Techniques 27: 1180-1186.
12. Boole, J. A. J. 1955. Studies in the anatomy of the family Celastraceae. Ph. D. thesis. Chapel Hill: University of North Carolina.
13. Bornstein, A. J. 1989. Celastraceae. Pp. 113-125 in Flora of the Lesser Antilles: leeward and windward islands vol. 5, ed. R. A. Howard Jamaica Plain: Arnold Arboretum.
14. Brizicky, G. K. 1964. The genera of Celastrales in the southeastern United States. Journal of the Arnold Arboretum 45: 206-234.
15. Bull, J. J., J. P. Huelsenbeck, C. W. Cunningham, D. L. Swofford, and P. J. Waddell. 1993. Partitioning and combining data in phylogenetic analysis. Systematic Biology 42: 384-397.
16. Castoe, T. A., T. M. Doan, and C. L. Parkinson. 2004. Data partitions and complex models in Bayesian analysis: the phylogeny of the gymnophthalmid lizards. Systematic Biology 53: 448-469. (Pubitemid 38946908)
17. Chase, M. W. and H. H. Hills. 1991. Silica gel: an ideal material for field preservation of leaf samples for DNA studies. Taxon 40: 215-220.
18. Coughenour, J. M., M. P. Simmons, J. A. Lombardi, and J. J. Cappa. 2010. Phylogeny of Celastraceae subfamily Salacioideae and tribe Lophopetaleae inferred from morphological characters and nuclear and plastid genes. Systematic Botany 35: 358-366.
19. Coughenour, J. M., M. P. Simmons, J. A. Lombardi, K. Yakobson, and R. H. Archer. 2011. Phylogeny of Celastraceae subfamily Hippocrateoideae inferred from morphological characters and nuclear and plastid genes. Molecular Phylogenetics and Evolution 59: 320-330.
20. Croizat, L. 1947. A study in the Celastraceae: Siphonodonoideae subf. nov. Lilloa 13: 31-43.
21. Davis, J. I., K. C. Nixon, and D. P. Little. 2005. The limits of conventional cladistic analysis. Pp. 119-147 in Parsimony, phylogeny, and genomics, ed. V. A. Albert. Oxford: Oxford University Press.
22. Davis, J. I., M. P. Simmons, D. W. Stevenson, and J. F. Wendel. 1998. Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atpA sequences. Systematic Biology 47: 282-310. (Pubitemid 128373237)
23. Ding Hou. 1963. Florae Malesianae precursores XXXIV notes on some genera of Celastraceae in Malaysia. Blumea 12: 31-38.
24. Ding Hou. 1964. Celastraceae - II. Pp. 389-421 in Flora Malesiana vol. 6, ed. C. G. G. J. van Steenis. Leyden: Flora Malesiana Foundation.
25. Doyle, J. J. 1992. Gene trees and species trees: molecular systematics as one-character taxonomy. Systematic Botany 17: 144-163.
26. Doyle, J. J. 1995. The irrelevance of allele tree topologies for species delimitation, and a non-topological alternative. Systematic Botany 20: 574-588.
27. Duan, H., Y. Takaishi, Y. Imakura, Y. Jia, D. Li, M. Cosentino, and K.-H. Lee. 2000. Sesquiterpene alkaloids from Tripterygium hypoglaucum and Tripterygium wilfordii: a new class of potent anti-HIV agents. Journal of Natural Products 63: 357-361. (Pubitemid 30173693)
28. Dunkley, H. L. and J. P. M. Brenan. 1948. Platypterocarpus, a new tree genus of Celastraceae from Tanganyika. Kew Bulletin 1948: 47-50.
29. Farris, J. S. 1989. The retention index and the rescaled consistency index. Cladistics 5: 417-419.
30. Farris, J. S., V. A. Albert, M. Källersjö, D. Lipscomb, and A. G. Kluge. 1996. Parsimony jackknifing outperforms neighbor-joining. Cladistics 12: 99-124.
31. Fawcett, W. and A. B. Rendle. 1926. Flora of Jamaica containing descriptions of the flowering plants known from the island. London: The British Museum.
32. Felsenstein, J. 1973. Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Systematic Zoology 22: 240-249.
33. Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Systematic Zoology 27: 401-410.
34. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
35. Gaut, B. S. and P. O. Lewis. 1995. Success of maximum likelihood phylogeny inference in the four-taxon case. Molecular Biology and Evolution 12: 152-162.
36. Gonzalez-Medrano, F. 1981. Rzedowskia, un nuevo genero de Celastraceae de Mexico. Boletín de la Sociedad Botánica de México 41: 41-46.
37. Gu, W.-Z. and S. R. Brandwein. 1998. Inhibition of type II collageninduced arthritis in rats by triptolide. International Journal of Immunopharmacology 20: 389-400. (Pubitemid 29034723)
38. Hudson, R. R. 1990. Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology 7: 1-44.
39. Huxley, A., M. Griffiths, and M. Levy. 1992. The new Royal Horticultural Society dictionary of gardening. London: MacMillan Press Limited.
40. Islam, M. B., M. P. Simmons, and R. H. Archer. 2006. Phylogeny of the Elaeodendron group (Celastraceae) inferred from morphological characters and nuclear and plastid genes. Systematic Botany 31: 512-524. (Pubitemid 44440935)
41. Jessup, L. W. 1984. Celastraceae. Pp. 150-180 in Flora of Australia vol. 22, ed. A. S. George. Canberra: Australian Government Publishing Service.
42. Joffily, A. and R. C. Vieira. 2006. Lectotypification of Goniodiscus elaeospermus and new synonyms for Maytenus (Celastroideae- Celastraceae) from Brazil. Kew Bulletin 61: 265-267. (Pubitemid 44701133)
43. Johnson, L. A. and D. E. Soltis. 1995. Phylogenetic inference in Saxifragaceae s. s. and Gilia (Polemoniaceae) using matK sequences. Annals of the Missouri Botanical Garden 82: 149-175.
44. Johnston, M. C. 1975. Synopsis of Canotia (Celastraceae) including a new species from the Chihuahuan Desert. Brittonia 27: 119-122.
45. Katoh, K. and H. Toh. 2008a. Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics 9: 286-298. (Pubitemid 351890825)
46. Katoh, K. and H. Toh. 2008b. Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFTbased framework. BMC Bioinformatics 9: 212.
47. Kluge, A. G. 1989. A concern for evidence and a phylogenetic hypothesis for relationships among Epicrates (Boidae, Serpentes). Systematic Zoology 38: 7-25.
48. Kluge, A. G. and J. S. Farris. 1969. Quantitative phyletics and the evolution of Anurans. Systematic Zoology 18: 1-32.
49. Kuhlmann, J. G. 1933. Novo genero de Celastraceas da flora amazonica. Archivos do Jardim Botanico do Rio de Janeiro 6: 109-110.
50. Kupchan, S. M., W. A. Court, R. G. Dailey, C. J. Gilmore, and R. F. Bryan. 1972. Triptolide and tripdiolide, novel antileukemic diterpenoid triepoxides from Tripterygium wilfordii. Journal of the American Chemical Society 94: 7194-7195.
51. 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. (Pubitemid 28113682)
52. Law, S. K.-Y.,M. P. Simmons, N. Techen, I. A. Khan, M.-F. He, P.-C. Shaw, and P. P.-H. But. 2011. Molecular analyses of the Chinese herb leigongteng (Tripterygium wilfordii Hook.f.). Phytochemistry 72: 21-26.
53. Lecointre, G. and P. Deleporte. 2005. Total evidence requires exclusion of phylogenetically misleading data. Zoologica Scripta 34: 101-117. (Pubitemid 40172130)
54. Lee, K. Y., W.-T. Chang, D. Qiu, P. N. Kao, and G. D. Rosen. 1999. PG490 (triptolide) cooperates with tumor necrosis factor-a to induce apoptosis in tumor cells. The Journal of Biological Chemistry 274: 13451-13455.
55. Lemmon, A. R., J. M. Brown, K. Stanger-Hall, and E. M. Lemmon. 2009. The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Systematic Biology 58: 130-145.
56. Loesener, T. 1942. Celastraceae. Pp. 87-197 in Die Natürlichen Pflanzenfamilien vol. 20b, eds. Engler A., H. Harms, and J. Mattfeld. Berlin: Duncker and Humblot.
57. Lundell, C. L. 1971. Studies of American plants-III. Wrightia 4: 153-172. Ma, J.-S., A. R. Brach, and Q.-R. Liu. 1999. A revision of the genus Tripterygium (Celastraceae). Edinburgh Journal of Botany 56: 33-46.
58. Maddison, D. R. and W. P. Maddison. 2001. MacClade: Analysis of phylogeny and character evolution version 4.03. Sunderland: Sinauer Associates.
59. McKenna, M. J., M. P. Simmons, R. H. Archer, C. D. Bacon, and J. A. Lombardi. 2011. Delimitation of the segregate genera of Maytenus s. l. (Celastraceae) based on morphological and molecular characters. Systematic Botany 36: 922-931.
60. Merrill, E. D. 1941. The Upper Burma plants collected by Captain K. Kingdon Ward on the Vernay-Cutting Expedition, 1938-39. Brittonia 4: 20-188.
61. Mory, B. 2001. Notes on Crossopetalum, Myginda and Gyminda (Celastraceae) from Cuba. Willdenowia 31: 129-135.
62. Müller, I. H. 1995. Systematics and leaf anatomy of the Celastraceae s. s. of New Caledonia. Ph. D. dissertation. Zürich: Universität Zürich.
63. Müller, K. 2006. Incorporating information from length-mutational events into phylogenetic analysis. Molecular Phylogenetics and Evolution 38: 667-676. (Pubitemid 43277592)
64. Nixon, K. C. and J. M. Carpenter. 1996. On simultaneous analysis. Cladistics 12: 221-242.
65. Perrier de la Bâthie, H. 1942. Révision des Célastracées de Madagascar et des Comores. Notulae Systematicae 10: 173-206.
66. Posada, D. 2008. jModelTest: phylogenetic model averaging. Molecular Biology and Evolution 25: 1253-1256. (Pubitemid 351882013)
67. Prigge, B. A. 1984. Studies on Acanthothamnus, Mortonia, and Orthosphenia (Celastraceae): anatomy, ecology, and systematics. Ph. D. thesis. Claremont: Claremont Graduate School.
68. Qiu, D., G. Zhao, Y. Aoki, L. Shi, A. Uyei, S. Nazarian, J. C.-H. Ng, and P. N. Kao. 1999. Immunosupressant PG490 (triptolide) inhibits T-cell interleukin-2 expression at the level of purine-box/nuclear factor of activated T-cells and NF-KB transcriptional activation. The Journal of Biological Chemistry 274: 13443-13450.
69. Rauscher, J. T., J. J. Doyle, and A. H. D. Brown. 2004. Multiple origins and nrDNA internal transcribed spacer homeologue evolution in the Glycine tomentella (Leguminosae) allopolyploid complex. Genetics 166: 987-998. (Pubitemid 38391756)
70. Rehder, A. 1934. Manual of cultivated trees and shrubs hardy in North America: exclusive of the subtropical and warmer temperate regions. New York: The MacMillan Company.
71. Rindal, E. and A. V. Z. Brower. 2011. Do model-based phylogenetic analyses perform better than parsimony? A test with empirical data. Cladistics 27: 331-334.
72. Robson, N. K. B., N. Hallé, B. Mathew, and R. Blakelock. 1994. Celastraceae. Pp. 1-78 in Flora of tropical East Africa vol. 108, ed. R. M. Polhill. Rotterdam: A. A. Balkema.
73. Rogstad, S. H. 1992. Saturated NaCl-CTAB solution as a means of field preservation of leaves for DNA analyses. Taxon 41: 701-708.
74. Rydberg, P. A. 1905. Family 4. Parnassiaceae. North American Flora 22: 77-80.
75. Sanderson, M. J. and J. Kim. 2000. Parametric phylogenetics? Systematic Biology 49: 817-829.
76. Sankoff, D. and P. Rousseau. 1975. Locating the vertices of a steiner tree in an arbitrary metric space. Mathematical Programming 9: 240-246.
77. Savinov, I. A. 2006. Some morphological basics for a revision of the tribe Celastreae Loes. (Celastraceae R. Br.). Wulfenia 13: 207-215.
78. Savolainen, V., M. F. Fay, D. C. Albach, A. Backlund, M. van der Bank, K. M. Cameron, S. A. Johnson, M. D. Lledó, J.-C. Pintaud, M. Powell, M. C. Sheanan, P. S. Soltis, D. E. Soltis, P. Weston, W. M. Whitten, K. J. Wurdack, and M. W. Chase. 2000. Phylogeny of the eudicots: a nearly complete familial analysis based on rbcL gene sequences. Kew Bulletin 55: 257-309.
79. Siddall,M. E. 1998. Success of parsimony in the four-taxon case: long-branch repulsion by likelihood in the Farris Zone. Cladistics 14: 209-220. (Pubitemid 128435230)
80. Simmons, M. P. 2004a. Celastraceae. Pp. 29-64 in The families and genera of flowering plants. VI. Flowering plants. Dicotyledons. Celastrales, Oxalidales, Rosales, Cornales, Ericales, ed. Kubitzki K. Berlin: Springer.
81. Simmons, M. P. 2004b. Parnassiaceae. Pp. 291-296 in The families and genera of flowering plants. VI. Flowering plants. Dicotyledons. Celastrales, Oxalidales, Rosales, Cornales, Ericales, ed. K. Kubitzki. Berlin: Springer.
82. Simmons, M. P. 2004c. Independence of alignment and tree search. Molecular Phylogenetics and Evolution 31: 874-879. (Pubitemid 38610960)
83. Simmons, M. P. 2012. Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data. Molecular Phylogenetics and Evolution 62: 472-484.
84. Simmons, M. P. and J. V. Freudenstein. 2002. Artifacts of coding amino acids and other composite characters for phylogenetic analysis. Cladistics 18: 354-365.
85. Simmons, M. P. and J. V. Freudenstein. 2003. The effects of increasing genetic distance on alignment of, and tree construction from, rDNA internal transcribed spacer sequences. Molecular Phylogenetics and Evolution 26: 444-451. (Pubitemid 36386501)
86. Simmons, M. P. and J. V. Freudenstein. 2011. Spurious 99% bootstrap and jackknife support for unsupported clades. Molecular Phylogenetics and Evolution 61: 177-191.
87. Simmons, M. P. and J. P. Hedin. 1999. Relationships and morphological character change among genera of Celastraceae s. l. (including Hippocrateaceae). Annals of the Missouri Botanical Garden 86: 723-757.
88. Simmons, M. P. and H. Ochoterena. 2000. Gaps as characters in sequencebased phylogenetic analyses. Systematic Biology 49: 369-381.
89. Simmons, M. P., C. D. Bailey, and K. C. Nixon. 2000. Phylogeny reconstruction using duplicate genes. Molecular Biology and Evolution 17: 469-473. (Pubitemid 30210693)
90. Simmons, M. P., M. J. McKenna, C. D. Bacon, J. J. Cappa, R. H. Archer, and A. J. Ford. 2012. Phylogeny of Celastraceae tribe Euonymeae inferred from morphological characters and nuclear and plastid loci. Molecular Phylogenetics and Evolution 62: 9-20.
91. Simmons,M. P., J. J. Cappa, R. H. Archer, A. J. Ford, D. Eichstedt, and C. C. Clevinger. 2008. Phylogeny of the Celastreae (Celastraceae) and the relationships of Catha edulis (qat) inferred from morphological characters and nuclear and plastid genes. Molecular Phylogenetics and Evolution 48: 745-757.
92. Simmons, M. P., C. C. Clevinger, V. Savolainen, R. H. Archer, S. Mathews, and J. J. Doyle. 2001a. Phylogeny of the Celastraceae inferred from phytochrome B and morphology. American Journal of Botany 88: 313-325. (Pubitemid 33703723)
93. Simmons, M. P., V. Savolainen, C. C. Clevinger, R. H. Archer, and J. I. Davis. 2001b. Phylogeny of the Celastraceae inferred from 26S nrDNA, phytochrome B, atpB, rbcL, and morphology. Molecular Phylogenetics and Evolution 19: 353-366. (Pubitemid 32566641)
94. Simmons, M. P., H. Ochoterena, and T. G. Carr. 2001c. Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses. Systematic Biology 50: 454-462.
95. Stamatakis, A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690. (Pubitemid 44642609)
96. Stamatakis, A. 2008. The RaxML 7.0.4 manual. Downloaded on 16 September 2008 from: http://icwww.epfl.ch/-stamatak/index-Dateien/ Page443.htm.
97. Steele, K. P. and R. Vilgalys. 1994. Phylogenetic analyses of Polemoniaceae using nucleotide sequences of the plastid gene matK. Systematic Botany 19: 126-142. (Pubitemid 2062255)
98. Stöver, B. C. and K. F. Müller. 2010. TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics 11: 7.
99. Swofford, D. L. 2001. PAUP*: Phylogenetic analysis using parsimony (*and other methods). Sunderland: Sinauer Associates.
100. 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.
101. Urban, I. 1904-1908. Celastraceae. Pp. 48-94 in Symbolae Antillanae seu Fundamenta Florae Indiae Occidentalis vol. 5, ed., I. Urban. Lipsiae: Fratres Borntraeger.
102. Wendel, J. F., A. Schnabel, and T. Seelanan. 1995. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proceedings of the National Academy of Sciences USA 92: 280-284.
103. White, T. J., T. Bruns, S. Lee, and J. Taylor. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Pp. 315-322 in PCR protocols: a guide to methods and applications, eds. Innis M., D. Gelfand, J. Sninsky and T. White. San Diego: Academic Press.
104. Wilkinson, M. 1995. A comparison of two methods of character construction. Cladistics 11: 297-308.
105. Yang, Z. 1993. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Molecular Biology and Evolution 10: 1396-1401.
106. Yang, Z. 2006. Computational molecular evolution. Oxford: Oxford University Press.
107. Yokoyama, J., M. Suzuki, K. Iwatsuki, and M. Hasebe. 2000. Molecular phylogeny of Coriaria, with special emphasis on the disjunct distribution. Molecular Phylogenetics and Evolution 14: 11-19. (Pubitemid 30457811)
108. Zhang, L.-B. and M. P. Simmons. 2006. Phylogeny and delimitation of the Celastrales inferred from nuclear and plastid genes. Systematic Botany 31: 122-137.
109. Zhang, L.-B., M. P. Simmons, A. Kocyan, and S. S. Renner. 2006. Phylogeny of the Cucurbitales based on DNA sequences of nine loci from three genomes: Implications for morphological and sexual system evolution. Molecular Phylogenetics and Evolution 39: 305-322.
110. Zurawski, G. and M. T. Clegg. 1987. Evolution of higher-plant chloroplast DNA-encoded genes: implications for structure-function and phylogenetic studies. Annual Review of Plant Physiology 38: 391-418.