Phylogeny of the genus Peperomia (Piperaceae) inferred from the trnK/matK region (cpDNA)

Plant Biology

Volumn 8, Issue 1, 2006, Pages 93-102

  Wanke, S ^a   Samain, M S ^b   Vanderschaeve, L ^b   Mathieu, G ^b   Goetghebeur, P ^b   Neinhuis, C ^a  

^a DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

^b GHENT UNIVERSITY   (Belgium)

Author keywords

Bayesian inference; Giant genera; matK; Peperomia; Phylogeny; trnK intron

Indexed keywords

CHLOROPLAST DNA;

PHYLOGENY;

ARTICLE; CLASSIFICATION; ENZYMOLOGY; GENE; GENETICS; INTRON; PEPEROMIA; PHYLOGENY; SEQUENCE ALIGNMENT;

DNA, CHLOROPLAST; GENES, PLANT; INTRONS; PEPEROMIA; PHYLOGENY; SEQUENCE ALIGNMENT;

MAGNOLIOPHYTA; PEPEROMIA; PIPERACEAE;

EID: 31644433398     PISSN: 14358603     EISSN: None     Source Type: Journal    
DOI: 10.1055/s-2005-873060     Document Type: Article

References (57)

1. Airy-Shaw, H. (1966) Diagnoses of new families, new names etc. for the seventh edition of Willis' Dictionary. Kew Bulletin 18, 249-273.
2. Airy-Shaw, H. (1987) Willis' Dictionary: A Dictionary of the Flowering Plants and Ferns (8th edition). Cambridge: Cambridge University Press.
3. APG1 (1998) An ordinal classification for the families of flowering plants. Annals of the Missouri Botanical Garden 85, 531-553.
4. APG2 (2003) An update of the Angiosperm Phylogey Group classification for the orders and families of flowering plants: APG II. Botanical Journal of the Linnean Society 141, 399-436.
5. Azuma, H., Thien, L. B., and Kawano, S. (1999) Molecular phylogeny of Magnolia (Magnoliaceae) inferred from cDNA sequences and evolutionary divergence of floral scents. Journal of Plant Research 112, 291-306.
6. Bornstein, A. J. (1991) The Piperaceae in the southeastern United States. Journal Arnold Arboretum (Suppl. 1), 349-366.
7. Borsch, T., Hilu, K. W., Quandt, D., Wilde, V., Neinhuis, C., and Barthlott W. (2003) Noncoding plastid trnT-trnF sequences reveal a well resolved phylogeny of Basal Angiosperms. Journal of Evolutionary Biology 16, 558-576.
8. Borsch, T., Löhne, C., Müller, K., Hilu, KW., Wanke, S., Worberg, A., Barthlott, W., Neinhuis, C., and Quandt, D. (2005) Towards understanding basal angiosperm diversification: recent insights using rapidly evolving genomic regions. Nora Acta Leopoldina 342, 85-110.
9. Bradley, U. (2002) Biogeography and speciation of the genus Peperomia Ruiz and Pavón in Eastern Polynesia. PhD thesis, University of Dublin, Trinity College.
10. Brummit, R. (1992) Vascular Plants, Families and Genera. Oxford: Clarendon Press.
11. Burger, W. (1971) Flora Costaricensis (family 41 Piperaceae). Fieldiana Botany 35, 5-79.
12. Burger, W. (1977) The Piperales and the monocots - alternate hypothesis for the origin of monocotyledonous flowers. The Botanical Review 43, 345-393.
13. Dahlstedt, H. (1900) Studien über süd- und central- amerikanische Peperomien mit besonderer Berücksichtigung der brasilianischen Sippen. Stockholm: Kongliga Svenska Vetenskaps - Akademiens handlingar 33.
14. de Candolle, C. (1923) Piperacearum clavis analytica. Candollea 1, 286-415.
15. Henschen, S. E. (1873) Études sur le Genre Peperomia Comprenant les Espèces de Caldas, Brésil, Acta Universitatis Upsaliensis. Nova acta Regiae Societatis Scientiarum Upsaliensis.
16. Heywood, V. (1978) Flowering Plants of the World. New York: Mayflower Books, Inc.
17. Hill, A. W. (1907) A revision of the geophilous species of Peperomia with some additional notes on their morphology and seedling structure. Annals of Botany 21, 141-160.
18. Hilu, K. W., Borsch, T., Müller, K., Soltis, D. E., Soltis, P. S., Savolainen, V., Chase, M. W., Powell, M. P., Alice, L. A., Evans, R., Sauquet, H., Neinhuis, C., Slotta, T. A. B., Rohwer, J. G., Campbell, C. S., and Chatrou, L. W. (2003) Angiosperm phylogeny based on matK sequence information. American Journal of Botany 90, 1758-1776.
19. Hilu, K. W. and Liang, H. (1997) The matK gene: sequence variation and application in plant systematics. American Journal of Botany 87, 830-839.
20. Huelsenbeck, J. P., Larget, B., Miller, R. E., and Ronquist, F. (2002) Potential applications and pitfalls of Bayesian inference of phylogeny. Systematic Biology 51, 673-688.
21. Huelsenbeck, J. P., Ronquist, F., Nielsen, R., and Bollback, J. P. (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294, 2310-2314.
22. Jaramillo, M. A., Manos, P. S., and Zimmer, E. A. (2004) Phylogenetic relationships of the perianthless Piperales: reconstructing the evolution of floral development. International Journal of Plant Sciences 165, 403-416.
23. Kelchner, S. A. (2002) Group II introns as phylogenetic tool: structure, function, and evolutionary constraints. American Journal of Botany 89, 1651-1669.
24. Liang, H. and Hilu, K. W. (1996). Application of the matK gene sequences to grass systematics. Canadian Journal of Botany 74, 125-134.
25. Löhne, C. and Borsch, T. (2005) Molecular evolution and phylogenetic utility of the petD group II intron: a case study in basal angiosperms. Molecular Biology and Evolution 22, 317-332.
26. Mathew, P. J. and Mathew, P. M. (2001) Pollen morphology of some members of Pipereaceae and its bearing on the systematics and phylogeny of the family. Rheedea 11, 65-78.
27. Miquel, F. A. W. (1843) Systema Piperacearum (Kramers, H. A., ed.), Rotterdam, pp.64-199.
28. Müller, K. (2004) PRAP - computation of Bremer support for large data sets. Molecular Phylogenetics and Evolution 31, 780-782.
29. Müller, K. (2005) SeqState - primer design and sequence statistics for phylogenetic DNA data sets. Applied Bioinformatics 4, 65-69.
30. Müller, K. and Borsch, T. (2005) Phylogenetics of Utricularia (Lentibulariceae) and molecular evolution of the trnK intron in a lineage with high substitutional rates. Plant Systematics and Evolution 250, 39-67.
31. Müller, K., Borsch, T., Legendre, L., Porembski, S., Theisen, I., and Barthlott, W. (2004) Evolution of Carnivory in Lentibulariaceae and the Lamiales. Plant Biology 6, 477-490.
32. Müller, J. and Müller, K. (2004) TreeGraph: automated drawing of complex tree figures using an extensible tree description format. Molecular Ecology Notes 4, 786-788.
33. Müller, J., Quandt, D., and Neinhuis, C. (2005). PhyDe - Phylogenetic Data Editor. Programm distributed by the author.
34. Neinhuis, C., Wanke, S., Hilu, K. W., Müller, K., and Borsch, T. (2004) Phylogeny of Aristolochiaceae based on parsimony, likelihood, and Bayesian analyses of trnL-trnF sequences. Plant Systematics and Evolution 250, 7-26.
35. Neuhaus, H. and Link, G. (1987) The chloroplast tRNA Lys (UUU) gene from mustard (Sinapis alba) contains a class II intron potentially coding for a maturase related polypeptide. Current Genetics 11, 251-257.
36. Nixon, K. C. (1999) The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15, 407-414.
37. Novak, F. (1954) System angiosperm. Preslia 26, 337-364.
38. Olmstead, R. G. and Palmer, J. (1994) Chloroplast DNA systematics: a review of methods and data analysis. American Journal of Botany 81, 1205-1224.
39. Posada, D. and Crandall, A. (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14, 817-818.
40. Rodriguez, F. J., Oliver, J. L., Marín, A., and Medina, J. R. (1990) The generic stochastic model of nucleotide substitution. Journal of Theoretical Biology 142, 485-501.
41. Ronquist, F. and Huelsenbeck, J. P. (2003) MRBAYES: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574.
42. Ruiz, H. and Pavón, J. (1794) Florae Peruvianae et Chilensis Prodromus. Madrid.
43. Sang, T., Crawford D. J., and Stuessy, T. F. (1997) Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). American Journal of Botany 84, 1120-1136.
44. Simmons, M. P. and Ochoterena, H. (2000) Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology 49, 369-381.
45. Skottsberg, C. (1947) The genus Peperomia in Chile. Acta Horti Gotoburgensis 17, 1-47.
46. Smith, A. C. (1981) Flora Vitiensis. Nova 2, 75-97.
47. Stehlé, H. (1940) Flore Descriptive des Antilles Françaises 2 - Les Pipérales. Fort-de-France: Imprimerie du Gouvernement.
48. Swofford, D. L. (1998) PAUP*. Phylogenetic Analysis Using Parsimony (*and other Methods). Sunderland: Sinauer Associates.
49. Tebbs, M. C. (1993) Piperaceae. In The Families and Genera of Vascular Plants (Kubitzki, K., ed.), Vol. 2. Flowering Plants - Dicotyledons - Magnoliid, Hamamelid and Caryophyllid Families. Berlin: Springer-Verlag.
50. Thorne, R. F. (1992). Classification and geography of the flowering plants. Botanical Review 58, 225-348.
51. Trelease, W. (1930) The geography of American peppers. Proceedings of the American Philosophical Society 69, 309-327.
52. Tucker, S. C., Douglas, A. W., and Liang, H. X. (1993) Utility of ontogenetic and conventional characters in determining phylogenetic relationships of Saururaceae and Piperaceae (Piperales). Systematic Botany 18, 614-641.
53. Walker, J. (1976a) Comparative pollen morphology and phylogeny of the Ranalean complex. In Origin and Early Evolution of Angiosperms (Beck, C., ed.), New York: Columbia University Press, pp.241-249.
54. Walker, J. (1976b) Evolutionary significance of the exine in the pollen of primitive angiosperms. In The Evolutionary Significance of the Exine (Fergusen, I. and Muller, J. eds.), London: Academic Press, pp.251-292.
55. Yuncker, T. G. (1933) Revision of the Hawaiian Species of Peperomia. Bulletin of the Bernice P. Bishop Museum, Honolulu, Hawaii, 112, 3-131, illust.
56. Yuncker, T. G. (1953) The Piperaceae of Argentina, Bolivia and Chile. Lilloa 27, 97-303.
57. Yuncker, T. G. (1974) The Piperaceae of Brasil III. Peperomia: taxa of uncertain status. Hoehnea 4, 71-413.