The molecular phylogeny of Alpinia (Zingiberaceae): A complex and polyphyletic genus of gingers

American Journal of Botany

Volumn 92, Issue 1, 2005, Pages 167-178

  Kress, W John ^a,b   Liu, Ai Zhong ^a   Newman, Mark ^c   Qing Jun, L I ^b  

^a DEPARTMENT OF PALEOBIOLOGY   (United States)

^b KEY LABORATORY OF TROPICAL FOREST ECOLOGY   (China)

^c ROYAL BOTANIC GARDEN EDINBURGH   (United Kingdom)

Author keywords

Alpinia; Flexistyly; Gingers; ITS; matK; Phylogeny; Tropical; Zingiberaceae

Indexed keywords

EVOLUTION; MOLECULAR ANALYSIS; PHYLOGENY; TAXONOMY;

ALPINIA; EMBRYOPHYTA; SIPHONOCHILUS; ZINGIBER OFFICINALE; ZINGIBERACEAE;

EID: 12244273055     PISSN: 00029122     EISSN: None     Source Type: Journal    
DOI: 10.3732/ajb.92.1.167     Document Type: Article

References (46)

1. BAKER, J. G. 1894. Order CXLIX. Scitamineae. In J. D. Hooker [ed.], Flora of British India, vol. VI, Orchideae to Cyperaceae, 198-264. L. Reeve & Co., London, UK.
2. BARRETT, S. C. H. 2002. Sexual inference of the floral kind. Heredity 88: 154-159.
3. CUI, X.-L., R.-C. WEI, AND R.-F. HUANG. 1996. A study on the breeding system of Amomum tsao-ko. In T.-L. Wu, Q.-G. Wu, and Z.-Y. Chen [eds.], Proceedings of the Second Symposium on the Family Zingiberaceae, 288-296. South China Institute of Botany, Guangzhou, P. R. China.
4. DE QUEIROZ, A., M. J. DONOGHUE, AND J. KIM. 1995. Separate versus combined analysis of phylogenetic evidence. Annual Review of Ecology and Systematics 26: 657-681.
5. 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.
6. FARRIS, J. S., M. KÄLLERSJÖ, A. G. KLUGE, AND C. BULT. 1994. Testing significance of incongruence. Cladistics 10: 315-319.
7. FELSENSTEIN, J. 1985. Confidence intervals on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
8. FUNAKOSHI, H., W. J. KRESS, J. SKORNICKOVA, A.-Z. LIU, AND K. INOUE. In press. Return from the lost: rediscovery of the presumed extinct Leptosolena (Zingiberaceae) in the Philippines and its phylogenetic placement in the gingers. Acta Phytotaxonomica et Geobotanica.
9. HARRIS, D. J., A. D. POULSEN, C. FRIMODT-MØLLER, J. PRESTON, AND Q. C. B. CRONK. 2000. Rapid radiation in Aframomum (Zingiberaceae): evidence from nuclear ribosomal DNA internal transcribed spacer (ITS) sequences. Edinburgh Journal of Botany 57: 377-395.
10. HOLTTUM, R. E. 1950. The Zingiberaceae of the Malay Peninsula. Gardener's Bulletin of Singapore 13: 1-249.
11. HULSENBECK, J. P., AND F. R. RONQUIST. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
12. JORDAN, S., C. SIMON, AND D. POLHEMUS. 2003. Molecular systematics and adaptive radiation of Hawaii's endemic damselfly genus Megalagrion (Odonata: Coenagrionidae). Systematic Biology 52: 89-109.
13. KRESS, W. J., AND C. D. SPECHT. In press. Between Cancer and Capricorn: phylogeny, evolution, and ecology of the tropical Zingiberales. In I. Friis and H. Balslev [eds.], Plant diversity and complexity patterns - local, regional and global dimensions. Biologiske Skrifter, The Royal Danish Academy of Sciences and Letters, Copenhagen, Denmark.
14. KRESS, W. J., L. M. PRINCE, AND K. J. WILLIAMS. 2002. The phylogeny and a new classification of the gingers (Zingiberaceae): evidence from molecular data. American Journal Botany 89: 1682-1696.
15. LARSEN, K., J. M. LOCK, H. MAAS, AND P. J. M. MAAS. 1998. Zingiberaceae. In K. Kubitzki [ed.], The families and genera of vascular plants, vol. 4, 474-495. Springer-Verlag, Berlin, Germany.
16. LI, Q.-J., Z.-F. XU, W. J. KRESS, Y.-M. XIA, L. ZHANG, X.-B. DENG, J.-Y. GAO, AND Z.-L. BAI. 2001. Flexible style that encourages outcrossing. Nature 410: 432.
17. LI, Q.-J., W. J. KRESS, Z.-F. XU, Y.-M. XIA, L. ZHANG, X.-B. DENG, AND J.-Y. GAO. 2002. Stigmatic behavior and the pollination biology of Alpinia kwangsiensis (Zingiberaceae). Plant Systematics and Evolution 232: 123-132.
18. LIAO, J.-P., AND Q.-G. WU. 1996. Fruit anatomy of Chinese Alpinia and its taxonomic significance. In T.-L. WU, Q.-G. WU, and Z.-Y. Chen [eds.], Proceedings of the 2nd Symposium on the Family Zingiberaceae, 82-90. Zhongshan University Press, Guangzhou, P. R. China.
19. MADDISON, D. R. 1991. The discovery and importance of multiple islands of most-parsimonious trees. Systematic Zoology 40: 315-328.
20. MANOS, P. S., AND K. P. STEELE. 1997. Phylogenetic analyses of "higher" Hamamelididae based on plastid sequence data. American Journal of Botany 84: 1407-1419.
21. MILLER, R. E., T. R. BUCKLEY, AND P. S. MANOS. 2002. An examination of the monophyly of morning glory taxa using Bayesian phylogenetic inference. Systematic Biology 51: 740-753.
22. MORT, M. E., P. S. SOLTIS, D. E. SOLTIS, AND M. L. MABRY. 2000. Comparison of three methods for estimating internal support for phylogenetic trees. Systematic Biology 49: 160-170.
23. NGAMRIABSAKUL, C., M. F. NEWMAN, AND Q. C. B. CRONK. 2000. Phylogeny and disjunction in Roscoea (Zingiberaceae). Edinburgh Journal of Botany 57: 39-61.
24. NIXON, K. C., AND J. M. CARPENTER. 1996. On simultaneous analysis. Cladistics 12: 221-241.
25. PEDERSEN, L. B. 2004. Phylogenetic analysis of the subfamily Alpinioideae (Zingiberaceae) with special emphasis on Etlingera Giseke, based on nuclear and plastid DNA. Plant Systematics and Evolution 245: 239-258.
26. POSADA, D., AND K. A. CRANDALL. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
27. RAMBAUT, A. 2000. Se-Al, version 2.0a3, Sequence alignment editor. University of Oxford, Oxford, UK.
28. RANGSIRUJI, A., M. F. NEWMAN, AND Q. C. B. CRONK. 2000a. Origin and relationshiups of Alpinia galanga (Zingiberaceae) based on molecular data. Edinburgh Journal of Botany 57: 9-37.
29. RANGSIRUJI, A., M. F. NEWMAN, AND Q. C. B. CRONK. 2000b. A study of the infrageneric classification of Alpina (Zingiberaceae) based on the ITS region of nuclear rDNA and the trnL-F spacer of chloroplast DNA. In K. L. Wilson and D. A. Morrison [eds.], Monocots - systematics and evolution, 695-709. CSIRO Publishing, Collingwood, Australia.
30. RENNER, S. S. 2001. How common is heterodichogamy? Trends in Ecology and Evolution 16: 595-597.
31. SCHUMANN, K. 1904. Zingiberaceae. In A. Engler [ed.], Das Pflanzenreich 4, 1-458. Leipzig, Germany.
32. SEARLE, R. J., AND T. A. J. HEDDERSON. 2000. A preliminary phylogeny of the Hedychieae tribe (Zingiberaceae) based on ITS sequences of the nuclear rRNA cistron. In K. L. Wilson and D. A. Morrison [eds.], Monocots - systematics and evolution, 710-718. CSIRO Publishing, Collingwood, Australia.
33. SMITH, R. M. 1975. A preliminary review of the large bracteate species of Alpinia. Notes from the Royal Botanic Garden Edinburgh 34: 149-182.
34. SMITH, R. M. 1990. Alpinia (Zingiberaceae): a proposed new infrageneric classification. Edinburgh Journal of Botany 47: 1-75.
35. STANFORD, A. M., R. HARDEN, AND C. R. PARKS. 2000. Phylogeny and biogeography of Juglans (Juglandaceae) based on matK and ITS sequence data. American Journal of Botany 87: 872-882.
36. STEELE, K. P., AND R. VILGALYS. 1994. Phylogenetic analyses of Polemoniaceae using nucleotide sequences of the plastid gene matK. Systematic Botany 19: 126-142.
37. SWOFFORD, D. L. 2002. PAUP*: phylogenetic analysis using parsimony (*and other methods), version 4.0b10. Sinauer, Sunderland, Massachusetts, USA.
38. TOYODA, T. 1981. Flora of Bonin Islands. Aboc-Sha, Kamakura, Japan.
39. VALETON, T. 1913. Zingiberaceae. Nova Guinea 8: 923-988.
40. VALETON, T. 1914. Die Zingiberaceen Deutsch-Neu-Guineas. Botanische Jahrbücher für Systematik, Pflanzengeschichte und Pflanzengeographie 52: 41-100.
41. WHITE, T. J., T. BRUNS, S. LEE, AND J. TAYLOR. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenies. In M. A. Innis, D. H. Gelfand, J. J. Sninsky, and T. J. White [eds.], PCR protocols: a guide to methods and applications, 315-322. Academic Press, San Diego, California, USA.
42. WILLIAMS, K. J., W J. KRESS, AND P. S. MANOS. 2004. The phylogeny, evolution, and classification of the genus Globba and tribe Globbeae (Zingiberaceae): appendages do matter. American Journal of Botany 91: 100-114.
43. WOOD, T. H., W. M. WHITTEN, AND N. H. WILLIAMS. 2000. Phylogeny of Hedychium and related genera (Zingiberaceae) based on ITS sequence data. Edinburgh Journal of Botany 57: 261-270.
44. WU, T.-L., AND K. LARSEN. 2000. Family Zingiberaceae. In Z.-G. Wu and P. H. Raven [eds.], Flora of China, vol. 24, 322-377. Science Press, Beijing, China, and Missouri Botanical Garden Press, St. Louis, Missouri, USA.
45. XIA, Y.-M., W. J. KRESS, AND L. M. PRINCE. 2004. A phylogenetic analysis of Amomum (Alpinioideae: Zingiberaceae) using ITS and matK DNA sequence data. Systematic Botany 29: 334-344.
46. ZHANG, L., Q.-J. LI, X.-B. DENG, P.-Y. REN, AND J.-Y. GAO. 2003. Reproductive biology of Alpinia blepharocalyx (Zingiberaceae): another example of flexistyly. Plant Systematics and Evolution 241: 67-76.