Molecular phylogeny and character evolution in terete-stemmed Andean opuntias (Cactaceae-Opuntioideae)

Molecular Phylogenetics and Evolution

Volumn 65, Issue 2, 2012, Pages 668-681

  Ritz, C M ^a   Reiker, J ^b   Charles, G ^c   Hoxey, P ^c   Hunt, D ^c   Lowry, M ^c   Stuppy, W ^d   Taylor, N ^e  

^a SENCKENBERG MUSEUM OF NATURAL HISTORY GÖRLITZ   (Germany)

^b JUSTUS LIEBIG UNIVERSITY   (Germany)

^c International Organization for Succulent Plant Study   (United Kingdom)

^d ROYAL BOTANIC GARDENS   (United Kingdom)

^e SINGAPORE BOTANIC GARDENS   (Singapore)

Author keywords

Andes; NrITS; Nuclear ribosomal DNA; Secondary structure; Seed anatomy; South America; Topological conflict

Indexed keywords

CHLOROPLAST DNA; PLANT DNA; RIBOSOMAL SPACER DNA;

ARTICLE; BAYES THEOREM; CACTACEAE; CELL NUCLEUS; CLASSIFICATION; CONFORMATION; DNA SEQUENCE; EVOLUTION; GENETICS; HISTOLOGY; PHYLOGENY; SEQUENCE ALIGNMENT; STATISTICAL MODEL;

BAYES THEOREM; BIOLOGICAL EVOLUTION; CACTACEAE; CELL NUCLEUS; DNA, CHLOROPLAST; DNA, PLANT; DNA, RIBOSOMAL SPACER; LIKELIHOOD FUNCTIONS; NUCLEIC ACID CONFORMATION; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

CACTACEAE; OPUNTIA; OPUNTIOIDEAE;

EID: 84866175260     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2012.07.027     Document Type: Article

References (77)

1. Alvarez I., Wendel J.F. Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogenet. Evol. 2003, 29:417-434.
2. Anderson E.F. The Cactus Family 2001, Timber Press, Portland, Oregon.
3. Anderson E.F. Das große Kakteenlexikon 2011, Eugen Ulmer, Suttgart, Germany. second ed.
4. Arakaki M., Soltis D.E., Speranza P. New chromosome counts and evidence of polyploidy in Haageocereus and related genera in tribe Trichocereeae and other tribes of Cactaceae. Brittonia 2007, 59:290-297.
5. Backeberg, C., 1958-62. Die Cactaceae. Gustav Fischer Verlag, Jena.
6. Backeberg, C., 1963. Descriptiones Cactearum Novarum.
7. Backeberg C. Das Kakteenlexikon 1966, Gustav Fischer Verlag, Jena.
8. Backeberg C., Knuth F.M. Kaktus-ABC. En haandbog for fagfolk og amatorer 1936, Nordisk Forlag, Copenhagen.
9. Bailey C.D., Carr T.G., Harris S.A., Hughes C.E. Characterization of angiosperm nrDNA polymorphism, paralogy, and pseudogenes. Mol. Phylogenet. Evol. 2003, 29:435-455.
10. Baldwin B.G., Sanderson M.J., Porter M.J., Wojciechowski M.F., Campbell C.S., Donoghue M.J. The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Ann. Missouri Bot. Gard. 1995, 82:247-277.
11. Bárcenas R.T., Yesson C., Hawkins J.A. Molecular systematics of the Cactaceae. Cladistics 2011, 27:1-20.
12. Barthlott W., Hunt D.R. Cactaceae. The Families and Genera of Vascular Plants 1993, 161-197. Springer Verlag, Berlin, Germany. K. Kubitzki, J.G. Rohwer, V. Bittrich (Eds.).
13. Britton N.L., Rose J.N. The Cactaceae 1919, Carnegie Institution, Washington DC.
14. Bruyns P.V., Mapaya R.J., Hedderson T. A new subgeneric classification for Euphorbia (Euphorbiaceae) in southern Africa based on ITS and psbA-trnH sequence data. Taxon 2006, 55:397-420.
15. Buckler E.S., Holtsford T.P. Zea ribosomal repeat evolution and substitution patterns. Mol. Biol. Evol. 1996, 13:623-632.
16. Doweld A.B. Tribal taxonomy of Pereskioideae and Opuntioideae (Cactaceae). Sukkulenty 1999, 1:25-26.
17. Edwards E.J., Donoghue M.J. Pereskia and the origin of the cactus life-form. Am. Nat. 2006, 167:777-793.
18. Edwards E.J., Nyffeler R., Donoghue M.J. Basal cactus phylogeny: implications of Pereskia (Cactaceae) paraphyly for the transition to the cactus life form. Am. J. Bot. 2005, 92:1177-1188.
19. Eickbush T.H., Eickbush D.G. Finely orchestrated movements: evolution of ribosomal RNA genes. Genetics 2007, 175:477-485.
20. Eggli U., Leuenberger B. On colour forms of Opuntia weberi (Cactaceae) with notes on the typification of the name. Willdenowia 1998, 28:175-180.
21. Endler J., Buxbaum F. Die Pflanzenfamilie der Kakteen 1974, Albrecht Philler Verlag, Minden, Germany. third ed.
22. Farris J.S., Kallersjo M., Kluge A.G., Bult C. Constructing a significance test for incongruence. Syst. Biol. 1995, 44:570-572.
23. Gibson A.C., Nobel P.S. The Cactus Primer 1986, Harvard University Press, Cambridge, Massachusetts, London, England.
24. Gilmer K., Thomas H.-P. Alte Bekannte, neu beschrieben: Cumulopuntia recurvata. Kakteen und andere Sukkulenten 2000, 52:85-92.
25. Grajales A., Aguilar C., Sanchez J.A. Phylogenetic reconstruction using secondary structures of internal transcribed spacer 2 (ITS2, rDNA): finding the molecular and morphological gap in Caribbean gorgonian corals. BMC Evol. Biol. 2007, 7.
26. Griffith M.P. Phylogenetic relationships in the Opuntioideae (Cactaceae) based on nrITS sequences. International Organization for Succulent Plant Study Bulletin 2002, 10:15-16.
27. Griffith M.P. What did the first cactus look like? An attempt to reconcile the morphological and molecular evidence. Taxon 2004, 53:493-499.
28. Griffith M.P., Porter J.M. Phylogeny of Opuntioideae (Cactaceae). Int. J. Plant Sci. 2009, 170:107-116.
29. Harpke D., Peterson A. Non-concerted ITS evolution in Mammilaria (Cactaceae). Mol. Phylogenet. Evol. 2006, 41:579-593.
30. Harpke D., Peterson A. Quantitative PCR revealed a minority of its copies to be functional in Mammillaria (Cactaceae). Int. J. Plant Sci. 2007, 168:1157-1160.
31. Harpke D., Peterson A. 5.8S motifs for the identification of pseudogenic ITS regions. Botany 2008, 86:300-305.
32. Harpke D., Peterson A. Extensive 5.8S nrDNA polymorphism in Mammillaria (Cactaceae) with special reference to the identification of pseudogenic internal transcribed spacer regions. J. Plant Res. 2008, 121:261-270.
33. Hartl W.P., Klapper H., Barbier B., Ensikat H.J., Dronskowski R., Müller P., Ostendorp G., Tye A., Bauer R., Barthlott W. Diversity of calcium oxalate crystals in Cactaceae. Can. J. Bot. 2007, 85:501-517.
34. Hartmann S., Nason J.D., Bhattacharya D. Extensive ribosomal DNA genic variation in the columnar cactus Lophocereus. J. Mol. Evol. 2001, 53:124-134.
35. Hartmann S., Nason J.D., Bhattacharya D. Phylogenetic origins of Lophocereus (Cactaceae) and the senita cactus-senita moth pollination mutualism. Am. J. Bot. 2002, 89:1085-1092.
36. Helsen P., Browne R., Anderson D., Verdyck P., van Dongen S. Galapagos Opuntia (prickly pear) cacti; extensive morphological diversity, low genetic variability. Biol. J. Linn. Soc. 2009, 96:451-461.
37. Hernández-Hernández T., Hernández H.M., De-Nova J.A., Puente R., Eguiarte L.E., Magallón S. Phylogenetic relationships and evolution of growth form in Cactaceae (Caryophyllales, Eucotyledoneae). Am. J. Bot. 2011, 98:44-61.
38. Hershkovitz M.A., Zimmer E.A. Conservation patterns in angiosperm rDNA ITS2 sequences. Nucleic Acids Res. 1996, 24:2857-2867.
39. Huelsenbeck J.P., Ronquist F. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 2001, 17:754-755.
40. Hunt D., Taylor N., Charles G. The new cactus lexicon 2006, Dh Books, Milborn Port.
41. Hunt D. Classification of the 'cylindroid' opuntias of South America. Cactaceae Systematics Initiatives 2011, 25:5-29.
42. Iliff J. The Andean opuntias: an annotated checklist of the indigenous non-platyopuntioid opuntias of South America. Succ. Plant Res. 2002, 6:133-244.
43. Jobes D.V., Thien L.B. A conserved motif in the 5.8S ribosomal RNA (rRNA) gene is a useful diagnostic marker for plant internal transcribed spacer (ITS) sequences. Plant Mol. Biol. Rep. 1997, 15:326-334.
44. Johnson A.J., Soltis D.E. MatK DNA sequences and phylogenetic reconstruction in Saxifragaceae s.str. Syst. Bot. 1994, 19:143-156.
45. Keller, A., Foerster, F., Mueller, T., Dandekar, T., Schultz, J., Wolf, M., 2010. Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees. Biology Direct 5.
46. Keller A., Schleicher T., Foerster F., Ruderisch B., Dandekar T., Mueller T., Wolf M. ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales). BMC Evol. Biol. 2008, 8.
47. Kiesling R. Puna, un género nuevo de Opuntiodeae (Cactaceae). Hickenia 1982, 55:289-294.
48. Kovařik A., MatyáŠek R., Lim K.Y., Skalická K., Koulaková B., Knapp S., Chase M.W., Leitch A.R. Concerted evolution of 18-5.8-26S rDNA repeats in Nicotiana allotetraploids. Biol. J. Linn. Soc. 2004, 82:615-625.
49. Kovařik A., Pires J.C., Leitch A.R., Lim K.Y., Sherwood A.M., MatyáŠek R., Rocca J., Soltis D.E., Soltis P.S. Rapid concerted evolution of nuclear ribosomal DNA in two Tragopogon allopolyploids of recent and recurrent origin. Genetics 2005, 169:931-944.
50. Las Peñas M.L., Urdampilleta J.D., Bernardello G., Forni-Martins E.R. Karyotypes, heterochromatin, and physical mapping of 18S-26S rDNA in Cactaceae. Cytogenet. Genome Res. 2009, 124:72-80.
51. Leuenberger B.E. Die Pollenmorphologie der Cactaceae. Dissertationes Botanicae 1976, 31:1-321.
52. Liu J.S., Schardl C.L. A conserved sequence in internal transcribed spacer-1 of plant nuclear ribosomal-RNA genes. Plant Mol. Biol. 1994, 26:775-778.
53. Maddison, W.P., Maddison, D.R., 2006. StochChar: A package of Mesquite modules for stochastic models of character evolution.
54. Maddison, W.P., Maddison, D.R., 2010. Mesquite: A modular system for evolutionary analysis. http://mesquiteproject.org.
55. Mai J.C., Coleman A.W. The internal transcribed spacer 2 exhibits a common secondary structure in green algae and flowering plants. J. Mol. Evol. 1997, 44:258-271.
56. Martins L. Systematics and biogeography of Klasea (Asteraceae-Cardueae) and a synopsis of the genus. Bot. J. Linn. Soc. 2006, 152:435-464.
57. Mauseth J.D. Tiny but complex foliage leaves occur in many "leafless" cacti (Cactaeceae). Int. J. Plant Sci. 2007, 168:845-852.
58. Mayol M., Rossello J.A. Why nuclear ribosomal DNA spacers (ITS) tell different stories in Quercus. Mol. Phylogenet. Evol. 2001, 19:167-176.
59. Nyffeler R. Phylogenetic relationships in the cactus family (Cactaceae) based on evidence from trnK/matK and trnL-trnF sequences. Am. J. Bot. 2002, 89:312-326.
60. Nyffeler R., Eggli U. A farewell to dated ideas and concepts - molecular phylogenetics and a revised suprageneric classification of the family Cactaceae. Schumannia 2010, 3:109-149.
61. Nylander, J.A.A., 2004. MrModeltest. Evolutionary Biology Centre, Uppsala University, Uppsala, Program distributed by the author.
62. Pinkava D.J. On the evolution of the continental North American Opuntioideae (Cactaceae). Succ. Plant Res. 2002, 6:59-98.
63. Ritz C.M., Schmuths H., Wissemann V. Evolution by reticulation: European dogroses originated by multiple hybridization across the genus Rosa. J. Hered. 2005, 96:4-14.
64. Robinson H. Scanning electron microscope studies in the spines and glochids of Opuntiodeae (Cactaceae). Am. J. Bot. 1974, 61:278-283.
65. Rowley G.D. Reunion of the genus Opuntia Mill. Natl. Cact. Succ. J. 1958, 13:3-6.
66. Sang T., Crawford D.J., Stuessy T.F. Documentation of reticulate evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA - implications for biogeography and concerted evolution. Proc. Natl. Acad. Sci. USA 1995, 92:6813-6817.
67. Schumann, K., 1897-1898. Gesamtbeschreibung der Cactaceae im Verhältnis zu ihrer systematischen Gliederung. Verlag J. Neumann, Neudamm.
68. Small R.L., Cronn R.C., Wendel J.F. Use of nuclear genes for phylogeny reconstruction in plants. Aust. Syst. Bot. 2004, 17:145-170.
69. Stamatakis A. RaxML-VI-HPC: Maximum Likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
70. Stuppy W. Seed characters and the classification of the Opuntioideae. Succ. Plant Res. 2002, 6:25-58.
71. Swofford, D.L., 2002. Paup* 4.0. Phylogenetic analyses using parsimony (and other methods). Sinauer Associates, Sunderland, Massachusetts.
72. Thornhill D.J., Lajeunesse T.C., Santos S.R. Measuring rDNA diversity in eucaryotic microbial systems: how intragenomic variation, pseudogenes, and PCR artifacts confound biodiversity estimates. Molec. Ecol. 2007, 16(5326):5340.
73. Von Hagen K.B., Kadereit J.W. The phylogeny of Gentianella (Gentianaceae) and its colonization of the southern hemisphere as revealed by nuclear and chloroplast DNA sequence variation. Org. Divers. Evol. 2001, 1:61-79.
74. Wallace R.S., Dickie S.L. Systematic implication of chloroplast DNA sequence variation in subfam. Opuntioideae (Cactaceae). Succ. Plant Res. 2002, 6:9-24.
75. Wendel J.F., Schnabel A., Seelanan T. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proc. Natl. Acad. Sci. USA 1995, 92:280-284.
76. Young I., Coleman A.W. The advantages of the ITS2 region of the nuclear rDNA cistron for analysis of phylogenetic relationships of insects: a Drosophila example. Mol. Phylogenet. Evol. 2004, 30:236-242.
77. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31:3406-3415.