An expanded plastid DNA phylogeny of Orchidaceae and analysis of jackknife branch support strategy

American Journal of Botany

Volumn 91, Issue 1, 2004, Pages 149-157

  Freudenstein, John V ^a   Van Den Berg, Cássio ^b   Goldman, Douglas H ^c   Kores, Paul J ^d   Molvray, Mia ^d   Chase, Mark W ^d  

^a OHIO STATE UNIVERSITY   (United States)

^b DEPARTAMENTO DE CIÊNCIAS BIOLÓGICAS   (Brazil)

^c HARVARD UNIVERSITY   (United States)

^d JODRELL LABORATORY   (United Kingdom)

Author keywords

Branch support; Jackknife analysis; matK; Orchidaceae; Phylogenetic analysis; Plastid DNA; rbcL

Indexed keywords

PHYLOGENETICS;

CYPRIPEDIOIDEAE; EMBRYOPHYTA; EPIDENDROIDEAE; ORCHIDACEAE; ORCHIDOIDEAE;

EID: 1642464904     PISSN: 00029122     EISSN: None     Source Type: Journal    
DOI: 10.3732/ajb.91.1.149     Document Type: Article

References (44)

1. BREMER, K. 1988. The limits of amino-acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42: 795-803.
2. BURNS-BALOGH, P., AND V. A. FUNK. 1986. A phylogenetic analysis of the Orchidaceae. Smithsonian Contributions to Botany 61.
3. CAMERON, K. M., M. W. CHASE, W. M. WHITTEN, P. J. KORES, D. C. JARRELL, V. A. ALBERT, T. YUKAWA, H. G. HILLS, AND D. H. GOLDMAN. 1999. A phylogenetic analysis of the Orchidaceae: evidence from rbcL nucleolide sequences. American Journal of Botany 86: 208-224.
4. CHASE, M. W., K. CAMERON, H. HILLS, AND D. JARRELL. 1994. DNA sequences and phylogenetics of the Orchidaceae and other lilioid monocots. In A. Pridgeon [ed.], Proceedings of the Fourteenth World Orchid Conference, 61-73. Her Majesty's Stationery Office, Glasgow, UK.
5. CHASE, M. W., ET AL. 2000. Higher-level systematics of the monocotyledons: an assessment of current knowledge and a new classification. In K. L. Wilson and D. A. Morrison [eds.], Monocots: systematics and evolution, 3-16. CSIRO Publishing, Collingwood, Victoria, Australia.
6. CLEMENTS, M. A., D. L. JONES, I. K. SGARMA, M. E. NIGHTINGALE, M. J. GARRATT, K. J. FITZGERALD, A. M. MACKENZIE, AND B. P. J. MOLLOY. 2002. Phylogenetics of Diurideae (Orchidaceae) based on the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA. Lindleyana 17: 135-171.
7. DEBRY, R. W., AND R. G. OLMSTEAD. 2000. A simulation study of reduced tree-search effort in boostrap resampling analysis. Systematic Biology 49: 171-179.
8. DRESSLER, R. L. 1981. The orchids: natural history and classification. Harvard University Press, Cambridge, Massachusetts, USA.
9. DRESSLER, R. L. 1990a. The major clades of the Orchidaceae - Epidendroideae. Lindleyana 5: 117-125.
10. DRESSLER, R. L. 1990b. The Neottieae in orchid classification. Lindleyana 5: 102-109.
11. DRESSLER, R. L. 1990c. The Spiranthoideae: grade or subfamily? Lindleyana 5: 110-116.
12. DRESSLER, R. L. 1993. Phylogeny and classilication of the orchid family. Timber Press, Portland, Oregon, USA.
13. FARRIS, J. S. 1969. A successive approximations approach to character weighting. Systematic Zoology 18: 374-385.
14. FARRIS, J. S. 1995. Jac. Computer program distributed by the author. Molekylärsystematiska laboratoriet, Naturhistoriska riksmuseet, Stockholm, Sweden.
15. FARRIS, J. S. 1997. Xac. Computer program distributed by the author. Molekylärsystematiska laboratoriet, Naturhistoriska riksmuseet, Stockholm, Sweden.
16. FARRIS, J. S., V. A. ALBERT, M. KÄLLERSJÖ, D. L. LIPSCOMB, AND A. G. KLUGE. 1996. Parsimony jackknifing outperforms neighbor-joining. Cladistics 12: 99-124.
17. FREUDENSTEIN, J. V. 1994. Gynostemium structure and relationships of the Corallorhizinae (Orchidaceae: Epidendroideae). Plant Systematics and Evolution 193: 1-19.
18. FREUDENSTEIN, J. V., AND M. W. CHASE. 2001. Analysis of mitochondrial nadlb-c intron sequences in Orchidaceae: utility and coding of length-change characters. Systematic Botany 26: 643-657.
19. FREUDENSTEIN, J. V., AND F. N. RASMUSSEN. 1997. Sectile pollinia and relationships in the Orchidaceae. Plant Systematics and Evolution 205: 125-146.
20. FREUDENSTEIN, J. V., AND F. N. RASMUSSEN. 1999. What does morphology tell us about orchid relationships? A cladistic analysis. American Journal of Botany 86: 225-248.
21. FREUDENSTEIN, J. V., C. VAN DEN BERGH, W. M. WHITTEN, K. M. CAMERON. D. H. GOLDMAN, AND M. W. CHASE. 2001. A multi-locus combined analysis of Epidendroideae (Orchidaceae). Botany 2001 meeting, Albuquerque, New Mexico, USA. (Abstract).
22. GOLDMAN, D. H., J. V. FREUDENSTEIN, P. J. KORES, M. MOLVRAY, D. C. JARRELL, W. M. WHITTEN, K. M. CAMERON, AND M. W. CHASE. 2001. Phylogenetics of Arethuseac (Orchidaceae) based on plastid matK and rbcL sequences. Systematic Botany 26: 670-695.
23. GOLOBOFF, P. 1993. NONA and PIWE. Version 2. American Museum of Natural History, New York, New York, USA.
24. GRAYBEAL, A. 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Systematic Biology 47: 9-17.
25. HEDGES, S. B. 1992. The number of replications needed for accurate estimation of the bootstrap p value in phylogenetic studies. Molecular Biology and Evolution 9: 366-369.
26. KÄLLERSJÖ, M., V. A. ALBERT, AND J. S. FARRIS. 1999. Homoplasy increases phylogenetic structure. Cladistics 15: 91-93.
27. KORES, P. J., M. MOLVRAY, P. H. WESTON, S. D. HOPPER, A. P. BROWN, K. M. CAMERON, AND M. W. CHASE. 2001. A phylogenetic analysis of Diurideaa (Orchidaceae) based on plastid DNA sequence data. American Journal of Botany 88: 1903-1914.
28. MØLLER, J. D., AND H. RASMUSSEN. 1984. Stegmata in Orchidales: character state distribution and polarity. Botanical Journal of the Linnean Society 89: 53-76.
29. MOLVRAY, M. P. J. KORES, AND M. W. CHASE. 2000. Polyphyly of mycoheterotrophic orchids and functional influences on floral and molecular characters. In K. L. Wilson and D. A. Morrison [eds.], Monocots: systematics and evolution, 441-448. CSIRO Publishing, Collingwood, Victoria, Australia.
30. MORT, M. E., P. S. SOLTIS, D. E. SOLTIS, AND M. L. MABRY. 2000. Comparison of three methods for estimating internal support on phylogenetic trees. Systematic Biology 49: 160-171.
31. NEYLAND, R., AND L. E. URBATSCH. 1995. A terrestrial origin for the Orchidaceae is suggested by a phylogeny inferred from ndhF chloroplast gene sequences. Lindleyana 10: 244-251.
32. NEYLAND, R., AND L. E. URBATSCH. 1996. Evolution in the number and position of fertile anthers in Orchidaceae inferred from ndhF chloroplast gene sequences. Lindleyana 11: 47-53.
33. NIXON, K. C. 2002. WinClada ver. 1.00.08. Published by the author, Ithaca, New York, USA.
34. POLLOCK, D. D., D. J. ZWICKL, J. A. MCGUIRE, AND D. M. HILLIS. 2002. Increased taxon sampling is advantageous for phylogenetic inference. Systematic Biology 51: 664-671.
35. RASMUSSEN, F. N. 1982. The gynostemium of the neottioid orchids. Opera Botanica 65: 1-96.
36. RUDALL, P. J., M. W. CHASE, D. F. CUTLER, J. RUSBY, AND A. Y. DE BRUIJN. 1998. Anatomical and molecular systematics of Asteliaceae and Hypoxidaceae. Botanical Journal of the Linnean Society 127: 1-42.
37. SAITOU, N., AND M. NEI. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4: 406-425.
38. SALAMIN, N. M. W. CHASE, T. R. HODKINSON, AND V. SAVOLAINEN. 2003. Assessing internal support with large phylogenetic DNA matrices. Molecular Phylogenetics and Evolution 27: 528-539.
39. SANDERSON, M. J. 1995. Objections to bootstrapping phylogenies: a critique. Systematic Biology 44: 299-320.
40. SENYO, D. M., AND J. V. FREUDENSTEIN. 2000. A molecular phylogeny of Corallorhiza and related genera. Botany 2000, Portland, Oregon, USA 6-10 August 2000 (Abstract).
41. SZLACHETKO, D. L. 1995. Systema orchidalium. Fragmenta Floristica et Geobotanica Supplementum 3: 1-152.
42. VAN DEN BERG, C., W. E. HIGGINS, R. L. DRESSLER, W. M. WHITTEN, M. A. SOTO ARENAS, A. CULHAM, AND M. W. CHASE. 2000. A phylogenetic analysis of Laeliinae (Orchidaceae) based on sequence data from internal transcribed spacers (ITS) of nuclear ribosomal DNA. Lindleyana 15: 96-114.
43. WENZEL, J. W., AND M. E. SIDDALL. 1999. Noise. Cladistics 15: 51-64.
44. WHITTEN, W. M., N. H. WILLIAMS, AND M. W. CHASE. 2000. Subtribal and generic relationships of Maxillarieae (Orchidaceae) with emphasis on Stanhopcinae: combined molecular evidence. American Journal of Botany 87: 1842-1856.