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PHYLOGENETICS OF PLEUROTHALLIDINAE:
resolving generic limits in a large group of small orchids



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REFERENCES

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Dressler, R. L. & N. H. Williams. 2000. Chelyorchis, a new genus. P. 1130 in Romero-González, G. A. and G. Carnevali Fernández-Concha. Orchids of Venezuela: An illustrated field guide. Second edition. Armitano Editores. Caracas, Venezuela.

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Entwisle, T.J. & P.H. Weston. 2005. Majority rules, when systematists disagree. Aust. Systematic Botany 18:1-6.

Farris, J. S., M. Källersjö, A.G. Kluge & C. Bult. 1994. Testing significance of incongruence. Cladistics 10:315-319.

Farris, J.S., V.A. Albert, M. Kallersjo, D. Lipscomb, & A.G. Kluge. 1996. Parsimony jackknifing outperforms neighbor-joining. Cladistics 12:99-124.

Freudenstein, J. V., C. van den Berg, D. H. Goldman, P. J. Kores, M. Molvray & M. W. Chase. 2004. An expanded plastid DNA phylogeny of Orchidaceae and analysis of jackknife branch support strategy. Am.J. Bot. 91:149-157.

Freudenstein, J.V. & M.W. Chase. 2001. Analysis of mitochondrial nad1b-c intron sequences in Orchidaceae: utility and coding of length-change characters. Syst. Bot. 26: 643-657.

Freudenstein, J. V. & M. W. Chase. 2003. Phylogenetic structure of the Orchidaceae based on multiple DNA loci and evaluation of key anther characters. Third International Conference on the Comparative Biology of the Monocotyledons, Ontario, CA.

Freudenstein, J. V. & F. N. Rasmussen. 1996. Pollinium development and number in the Orchidaceae. Am. J. Bot. 83:813-824.

Freudenstein, J. V. & F. N. Rasmussen. 1999. What does morphology tell us about orchid relationships? -- A cladistic analysis. Am. J. Bot. 86:225-248.

Freudenstein, J. V., F. N. Rasmussen & E. M. Harris. 2002. The evolution of anther morphology in orchids - incumbent anthers, superposed pollinia, and the vandoid complex. Am. J. Bot. 89:1747-1755.

Freudenstein, J. V., C. van den Berg, D. H. Goldman, P. J. Kores, M. Molvray & M. W. Chase. 2004. An expanded plastid DNA phylogeny of Orchidaceae and analysis of jackknife branch support strategy. Am. J. Bot. 91:149-157.

Goldman, D., J. Freudenstein, P. Kores, M. Molvray, D. Jarell, W. M. Whitten, K. Cameron, R. Jansen, & M. W. Chase. 2001. Phylogenetics of Arethuseae (Orchidaceae) based on plastid matK and rbcL sequences. Syst. Bot. 26:670-695.

Goloboff, P.A. 1999. Analyzing large data sets in reasonable times: Solutions for composite optima. Cladistics 15:415-428.

Goloboff, P., S. Farris, & K. Nixon. 2000. TNT (Tree analysis using New Technology) (BETA). Published by the authors, Tucumán, Argentina.

Graybeal, A. 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol. 74:9-17.

Higgins, W. E. 2000. Intergeneric and intrageneric phylogenetic relationships of Encyclia (Orchidaceae) based upon holomorphology. Doctoral dissertation, Horticultural Sciences. Gainesville, University of Florida: 297 pp.

Higgins, W. E. (in press). Holomorphology: The total evidence approach to phylogenetic reconstruction. Proceedings of the 18th World Orchid Conference.

Hillis, D. M. 1996. Inferring complex phylogenies. Nature 383:130-131.

Ibisch, P. L., C. Nowicki, R. Muller, & N. Araujo. 2003. Methods for the assessment of habitat and species conservation in data-poor countries - case study of Pleurothallidinae (Orchidaceae) of the Andean rain forests of Bolivia. Lyonia 2:109-132.

Jones, T.R., A.G. Kluge, & A.J. Wolf. 1993. When theories and methodologies clash. Syst. Biol. 42: 92-102.

Jørgensen P.M, S. León-Yánez. 1999. Catalogue of the Vascular Plants of Ecuador. Missouri Botanical Garden. Missouri. U.S.A.

Jost, L. & L. Endara 2004. Analysis of the DNA-Based reclassification of the Pleurothallidinae. http://www.loujost.com/DNAFrameset/DNAanalysisDocument.htm

Källersjö, M., V.A. Albert, & J.S. Farris. 1999. Homoplasy increases phylogenetic structure. Cladistics 15:91-93.

Kolaczkowski, B. & J.W. Thornton. 2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature (London) 431: 980-984.

Kluge, A.G. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Sys. Zoology 38: 7-25.

Kluge, A.G. & A.J. Wolf. 1993. Cladistics-What's in a word. Cladistics 9:183-199.

Koehler, S., N. H. Williams, W. M. Whitten, & M. E. do Amaral. 2002. Phylogeny of the Bifrenaria Lindl. (Orchidaceae) complex based on morphology and sequence data from nuclear rDNA internal transcribed spacer (ITS) and chloroplast trnL-F region. International Journal of Plant Sciences 163:1055-1066.

Kron, K. A., & W. S. Judd. 1997. Systematics of the Lyonia group (Andromedeae, Ericaceae) and the use of species as terminals in higher-level cladistic analyses. Syst. Bot. 22:479-492.

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Kurzweil, H. 1988. Developmental studies in orchid flowers III: Neottioid species. Nordic J. Botany 8:271-282.

Lecointre, G., H. Philippe, et al. 1993. Species sampling has a major impact on phylogenetic inference. Mol. Phylogenet. Evol. 2:205-224.

Lecointre, G., H. Philippe, et al. 1994. How many nucleotides are required to resolve a phylogenetic problem? The use of a new statistical method applicable to available sequences. Mol. Phylogenet. Evol. 3:292-309.

Lloyd, D.G. & V.L. Calder. 1991. Multi-residue gaps, a class of molecular characters with exceptional reliability for phylogenetic analyses. J. Evolutionary Biology 4:9-21.

Luer, C.A. 1985. A key to the genera of the Pleurothallidinae. Pp. 239-245 in Proceedings of the Eleventh World Orchid Conference. Kiat Tan, ed. Published by the Eleventh WOC, Miami.

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Pridgeon, A.M., R. Solano, & M.W. Chase. 2001. Phylogenetic relationships in Pleurothallidinae (Orchidaceae): combined evidence from nuclear and plastid DNA sequences. Am. J. Bot. 88:2286-2308.

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Rokas, A. & S.B. Carroll. 2005. More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol. Biol. Evol. 22:1337-1344.

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