Molecular phylogenetics and morphological evolution of St. John's wort (Hypericum; Hypericaceae)

Molecular Phylogenetics and Evolution

Volumn 66, Issue 1, 2013, Pages 1-16

  Nürk, Nicolai M ^a   Madriñán, Santiago ^b   Carine, Mark A ^c   Chase, Mark W ^d   Blattner, Frank R ^a  

^a LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

^b UNIVERSIDAD DE LOS ANDES   (Colombia)

^c DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

^d ROYAL BOTANIC GARDENS   (United Kingdom)

Author keywords

Character evolution; Hypericaceae; Internal transcribed spacer (ITS); Phylogeny; Thornea; Triadenum

Indexed keywords

PLANT DNA; RIBOSOMAL SPACER DNA;

AFRICA; ARTICLE; BAYES THEOREM; CLASSIFICATION; DNA SEQUENCE; EVOLUTION; GENETICS; HYPERICUM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SOUTH AMERICA;

AFRICA; BAYES THEOREM; BIOLOGICAL EVOLUTION; DNA, PLANT; DNA, RIBOSOMAL SPACER; HYPERICUM; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SOUTH AMERICA;

CLUSIACEAE; HYPERICUM; THORNEA; TRIADENUM;

EID: 84870247627     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2012.08.022     Document Type: Article

References (67)

1. Akaike, H., 1974. New look at statistical-model identification. IEEE Trans. Autom. Contr. AC 19, 716-723.
2. Álvarez I., Wendel J.F. Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogenet. Evol. 2003, 29:417-434.
3. Apg I.I.I. An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: APG III. Bot. J. Linn. Soc. 2009, 161:105-121.
4. Baldwin B.G. Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from the compositae. Mol. Phylogenet. Evol. 1992, 1:3-16.
5. Baldwin B.G., Sanderson M.J., Porter J.M., 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.
6. Bänfer G., Moog U., Fiala B., Mohamed M., Weising K., Blattner F.R. A chloroplast genealogy of myrmecophytic Macaranga species (Euphorbiaceae) in Southeast Asia reveals hybridization, vicariance and long-distance dispersals. Mol. Ecol. 2006, 15:4409-4424.
7. Blattner F.R. Direct amplification of the entire ITS region from poorly preserved plant material using recombinant PCR. Biotechniques 1999, 27:1180-1186.
8. Blattner F.R. Phylogenetic analysis of Hordeum (Poaceae) as inferred by nuclear rDNA ITS sequences. Mol. Phylogenet. Evol. 2004, 33:289-299.
9. Blattner F.R., Weising K., Bänfer G., Maschwitz U., Fiala B. Molecular analysis of phylogenetic relationships among myrmecophytic Macaranga species (Euphorbiaceae). Mol. Phylogenet. Evol. 2001, 19:331-344.
10. Brassac J., Jakob S.S., Blattner F.R. Progenitor-derivative relationships of Hordeum polyploids (Poaceae, Triticeae) inferred from sequences of TOPO6, a nuclear low-copy gene region. PLoS ONE 2012, 7:e33808.
11. Butterweck V. Mechanism of action of St. John's wort in depression - What is known?. CNS Drugs 2003, 17:539-562.
12. Butterweck V., Schmidt M. St. John's wort: role of active compounds for its mechanism of action and efficacy. WMW 2007, 157:356-361.
13. Carine M.A., Christenhusz M.J.M. About this volume: the monograph of Hypericum by Norman Robson. Phytotaxa 2010, 4:1-4.
14. Chase M.W., Hills H.G. Silica gel: an ideal material for field preservation of leaf samples for DNA studies. Taxon 1991, 40:215-220.
15. Crockett S.L., Robson N.K. Taxonomy and chemotaxonomy of the genus Hypericum. Med. Aromat. Plant. Sci. Biotechnol. 2011, 5:1-13.
16. Crockett S.L., Douglas A.W., Scheffler B.E., Khan I.A. Genetic profiling of Hypericum (St. John's wort) species by nuclear ribosomal ITS sequence analysis. Plant. Med. 2004, 70:929-935.
17. Curtis J., Lersten N. Internal secretory structures in Hypericum (Clusiaceae): H. perforatum L. and H. balearicum L. New Phytol. 1990, 114:571-580.
18. Doyle J.J., Doyle J.L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 1987, 19:11-15.
19. Doyle J.J., Doyle J.L. Isolation of plant DNA from fresh tissue. Focus 1990, 12:13-15.
20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
21. Gustafsson M., Bittrich V., Stevens P.F. Phylogeny of clusiaceae based on rbcL sequences. Int. J. Plant. Sci. 2002, 163:1045-1054.
22. Heenan P.B. Three newly recognised species of Hypericum (Clusiaceae) from New Zealand. New Zealand J. Bot. 2008, 46:547-558.
23. Huelsenbeck J.P. Performance of phylogenetic methods in simulation. Syst. Biol. 1995, 44:17-48.
24. Jakob S.S., Blattner F.R. A chloroplast genealogy of Hordeum (Poaceae): long-term persisting haplotypes, incomplete lineage sorting, regional extinction, and the consequences for phylogenetic inference. Mol. Biol. Evol. 2006, 23:1602-1612.
25. Karppinen K., Hokkanen J., Mattila S., Neubauer P., Hohtola A. Octaketide-producing type III polyketide synthase from Hypericum perforatum is expressed in dark glands accumulating hypericins. Febs J. 2008, 275:4329-4342.
26. Koch M.A., Dobeš C., Mitchell-Olds T. Multiple hybrid formation in natural populations: concerted evolution of the internal transcribed spacer of nuclear ribosomal DNA (ITS) in North American Arabis divaricarpa (Brassicaceae). Mol. Biol. Evol. 2003, 20:338-350.
27. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., Higgins D.G. Clustal W and clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
28. Matzk F., Hammer K., Schubert I. Coevolution of apomixis and genome size within the genus Hypericum. Sex. Pl. Reprod. 2003, 16:51-58.
29. Myers O.J. Megasporogenesis, megagametophyte development and endosperm development in Hypericum virginicum. Am. J. Bot. 1964, 51:664.
30. Nieto Feliner G., Gutiérrez Larena B., Fuertes Aguilar J. Fine-scale geographical structure, intra-individual polymorphism and recombination in nuclear ribosomal internal transcribed spacers in Armeria (Plumbaginaceae). Ann. Bot. 2004, 93:189-200.
31. Nürk N.M., Blattner F.R. Cladistic analysis of morphological characters in Hypericum (Hypericaceae). Taxon 2010, 59:1495-1507.
32. Pagel M. Inferring the historical patterns of biological evolution. Nature 1999, 401:877-884.
33. Pagel M., Meade A., Barker D. Bayesian estimation of ancestral character states on phylogenies. Syst. Biol. 2004, 53:673-684.
34. Park S.J., Kim K.J. Molecular phylogeny of the genus Hypericum (Hypericaceae) from Korea and Japan: evidence from nuclear rDNA ITS sequence data. J. Plant Biol. 2004, 47:366-374.
35. Pilepic K.H., Morovic M., Orac F., Santor M., Vejnovic V. RFLP analysis of cpDNA in the genus Hypericum. Biologia 2010, 65:805-812.
36. Pilepic K., Balic M., Blazina N. Estimation of phylogenetic relationships among some Hypericum (Hypericaceae) species using internal transcribed spacer sequences. Plant Biosyst. 2011, 145:81-87.
37. Posada D., Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
38. R Development Core Team, 2011. R. R Foundation for Statistical Computing, Vienna, Austria http://www.R-project.org.
39. Rambaut, A., 2006-2009. FigTree v1.3.1. http://www.tree.bio.ed.ac.uk/software/figtree/.
40. Rieseberg L.H., Soltis D.E. Phylogenetic consequences of cytoplasmic gene flow in plants. Evol. Trends Plant 1991, 5:65-84.
41. Robba L., Carine M.A., Russell S., Raimondo F. The monophyly and evolution of Cynara L. (Asteraceae) sensu lato: evidence from the internal transcribed spacer region of nrDNA. Plant Syst. Evol. 2005, 253:53-64.
42. Robson N.K.B. Studies in the genus Hypericum L. (Guttiferae): 1. Infrageneric classification. Bull. Brit. Mus. (Nat. Hist.) Bot. 1977, 5:291-355.
43. Robson N.K.B. Studies in the genus Hypericum L. (Guttiferae): 2. Characters of the genus. Bull. Brit. Mus. (Nat. Hist.) Bot. 1981, 8:55-226.
44. Robson N.K.B. Studies in the genus Hypericum L. (Guttiferae): 3. Sections 1. Campylosporus to 6a. Umbraculoides. Bull. Brit. Mus. (Nat. Hist.) Bot. 1985, 12:1-325.
45. Robson N.K.B. Studies in the genus Hypericum L. (Guttiferae): 7. Section 29. Brathys (part 1). Bull. Brit. Mus. (Nat. Hist.) Bot. 1987, 16:1-106.
46. Robson N.K.B. Studies in the genus Hypericum L. (Guttiferae): 8. Sections 29. Brathys (part 2) and 30. Trigynobrathys. Bull. Nat. Hist. Mus. Lond. Bot. 1990, 20:1-151.
47. Robson N.K.B. Parallel evolution in tropical montane Hypericum. Opera Bot. 1993, 121:263-274.
48. Robson N.K.B. Studies in the genus Hypericum L. (Guttiferae) 4(1). Sections 7. Roscyna to 9. Hypericum sensu lato (part 1). Bull. Nat. Hist. Mus. Lond. Bot. 2001, 31:37-88.
49. Robson N.K.B. Hypericum botany. Hypericum - The Genus Hypericum 2003, 1-22. Taylor and Francis, London, New York. E. Ernst (Ed.).
50. Robson N.K.B. Studies in the genus Hypericum L. (Clusiaceae). Section 9. Hypericum sensu lato (part 3): subsection 1. Hypericum series 2. Senanensia, subsection 2. Erecta and section 9b. Graveolentia. Syst. Biodivers. 2006, 4:19-98.
51. Robson N.K.B. Studies in the genus Hypericum L (Hypericaceae) 5(2). Sections 17. Hirtella to 19. Coridium. Phytotaxa 2010, 4:127-258.
52. Robson N.K.B. Studies in the genus Hypericum L. (Hypericaceae) 5(1). Sections 10. Olympia to 15/16. Crossophyllum. Phytotaxa 2010, 4:5-126.
53. Ronquist F., Huelsenbeck J.P. MrBayes 3: bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
54. Ruhfel B., Bittrich V., Bove C., Gustafsson M., Philbrick C., Rutishauser R., Xi Z., Davis C. Phylogeny of the clusioid clade (Malpighiales): evidence from the plastid and mitochondrial genomes. Am. J. Bot. 2011, 98:306-325.
55. Schallau A., Arzenton F., Johnston A.J., Hahnel U., Koszegi D., Blattner F.R., Altschmied L., Haberer G., Barcaccia G., Bäumlein H. Identification and genetic analysis of the APOSPORY locus in Hypericum perforatum L. Plant J 2010, 62:773-784.
56. Shimodaira H. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 2002, 51:492-508.
57. Shimodaira H., Hasegawa M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 2001, 17:1246-1247.
58. Sirvent T.M., Krasnoff S.B., Gibson D.M. Induction of hypericins and hyperforins in Hypericum perforatum in response to damage by herbivores. J. Chem. Ecol. 2003, 29:2667-2681.
59. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
60. Stech M., Quandt D. 20,000 species and five key markers: the status of molecular bryophyte phylogenetics. Phytotaxa 2010, 9:196-228.
61. Stevens P.F. Hypericaceae. The Families and Genera of Vascular Plants 2007, 194-201. Springer Verlag, Berlin, Heidelberg. K. Kubitzki (Ed.).
62. * and Other Methods) 2002, Sinauer Associates, Sunderland.
63. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The clustal X windows interface. Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acid Res. 1997, 25:4876-4882.
64. Wurdack K.J., Davis C.C. Malpighiales phylogenetics: gaining ground on one of the most recalcitrant clades in the angiosperm tree of life. Am. J. Bot. 2009, 96:1551-1570.
65. Wurglics M., Schubert-Zsilavecz M. Hypericum perforatum: a 'modern' herbal antidepressant - pharmacokinetics of active ingredients. Clin. Pharmacokinet. 2006, 45:449-468.
66. Zouhar, K., 2004. Hypericum perforatum. In: F.S.L. (Ed.), Fire Effects Information System. Rocky Mountain Research Station. US Department of Agriculture, Forest Service.
67. Zwickl D.J., Hillis D.M. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 2002, 51:588-598.