Molecular phylogeny of Gavilea (Chloraeinae: Orchidaceae) using plastid and nuclear markers

Molecular Phylogenetics and Evolution

Volumn 62, Issue 3, 2012, Pages 889-897

  Chemisquy, M Amelia ^a   Morrone, Osvaldo ^a  

^a Facultad de Ciencias Naturales e Instituto M Lillo   (Argentina)

Author keywords

AtpB rbcL; Chloraeinae; Gavilea; MatK trnK; Molecular phylogeny; NrITS; RpoC1; South American orchids

Indexed keywords

RIBOSOMAL SPACER DNA;

ARTICLE; CHEMISTRY; CLASSIFICATION; GENETICS; ORCHIDACEAE; PHYLOGENY; PLASTID;

DNA, RIBOSOMAL SPACER; ORCHIDACEAE; PHYLOGENY; PLASTIDS;

BIPINNULA; CHLORAEA; CHLORAEINAE; CRANICHIDEAE; GAVILEA; ORCHIDACEAE;

EID: 84856285302     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2011.11.026     Document Type: Article

References (48)

1. álvarez-Molina A., Cameron K.M. Molecular phylogenetics of Prescottiinae s.l. and their close allies (Orchidaceae, Cranichideae) inferred from plastid and nuclear ribosomal DNA sequences. Am. J. Bot. 2009, 96:1020-1040.
2. Bailey C.D., Carr T.G., Harris S.A., Hughes C.E. Characterization of angiosperm nrDNA polymorphism, paralogy, and pseudogenes. Mol. Phylogenet. Evol. 2003, 29:435-455.
3. Barkman T.J., Simpson B.B. Hybrid origin and parentage of Dendrochilum acuiferum (Orchidaceae) inferred in a phylogenetic context using nuclear and plastid DNA sequence data. Syst. Bot. 2002, 27:209-220.
4. Brinegar C. Assessing evolution and biodiversity in plants at the molecular level. Kathmandu Univ. J. Sci., Eng. Technol. 2009, 5:149-159.
5. Cameron K.M. A comparison and combination of plastid atpB and rbcL gene sequences for inferring phylogenetic relationships within Orchidaceae. Aliso 2006, 22:447-464.
6. Cameron K.M., Chase M.W., Whitten W.M., Kores P.J., Jarrell D.C., Albert V.A., Yukawa T., Hills H.G., Goldman D.H. A phylogenetic analysis of the Orchidaceae: evidence from rbcL nucleotide sequences. Am. J. Bot. 1999, 86:208-224.
7. Chase M.W. Classification of Orchidaceae in the age of DNA data. Curtis's Bot. Mag. 2005, 22:2-7.
8. Chemisquy M.A. Novedades nomenclaturales en el género Gavilea (Orchidaceae, Chloraeinae), con especial énfasis en las especies chilenas. Darwiniana 2009, 47:315-320.
9. Chemisquy M.A. Las orquídeas del género Gavilea Poepp.: sistemática, taxonomía, biogeografía y conservación. Tesis Doctoral 2010, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires.
10. Chemisquy M.A., Morrone O. Phylogenetic analysis of the subtribe Chloraeinae (Orchidaceae): a preliminary approach based on three chloroplast markers. Aust. Syst. Bot. 2010, 23:38-46.
11. Clements M.A., Jones D.L., Sharma I.K., Nightingale M.E., Garratt M.J., Fitzgerald K.J., Mackenzie A.M., Molloy B.P.J. Phylogenetics of Diurideae (Orchidaceae) based on the Internal Transcribed Spacer (ITS) regions of nuclear ribosomal DNA. Lindleyana 2002, 17:135-171.
12. Clements M.A., Otero J.T., Miller J.T. Phylogenetic relationships in Pterostylidinae (Cranichideae: Orchidaceae): combined evidence from nuclear ribosomal and plastid DNA sequences. Aust. J. Bot. 2011, 59:99-117.
13. Correa M.N. Las especies argentinas del género Gavilea. Bol. Soc. Argent. Bot. 1956, 6:73-86.
14. Correa M.N. Una especie nueva y algunas observaciones críticas del género Gavilea (Orchidaceae). Bol. Soc. Argent. Bot. 1966, 11:60-66.
15. Correa M.N. Chloraea, género sudamericano de Orchidaceae. Darwiniana 1969, 15:374-500.
16. Corriveau J.L., Coleman A.W. Rapid screening method to detect potential biparental inheritance of plastid DNA and results for over 200 angiosperm species. Am. J. Bot. 1988, 75:1443-1458.
17. Domínguez, E., 2004. Catálogo preliminar de la familia Orchidaceae del Parque Nacional Torres del Paine, XII Región, Chile. Chloris Chilensis, año 7; No. 1. http://www.chlorischile.cl.
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. Dressler R.L. The Orchids. Natural History and Classification 1981, Harvard University Press, Cambridge, Massachusetts.
20. Dressler R.L. Phylogeny and Classification of the Orchid Family 1993, Dioscorides Press, Portland.
21. Feliner G.N., Roselló J.A. Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Mol. Phylogenet. Evol. 2007, 44:911-919.
22. Felsenstein, J., 1993. DNADIST Version 3.5c - Program to Compute Distance Matrix from Nucleotide Sequences. © Copyright 1986-1993 by Joseph Felsenstein and the University of Washington.
23. Freudenstein J.V., van den Berg C., Goldman D.H., Kores P.J., Molvray M., Chase M.W. An expanded plastid DNA phylogeny of Orchidaceae and analysis of jackknife branch support strategy. Am. J. Bot. 2004, 91:149-157.
24. Funk D.J., Omland K.E. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu. Rev. Ecol. Evol. Syst. 2003, 34:397-423.
25. Goloboff P.A., Farris J.S., Källersjö M., Oxelman B., Ramírez M.J., Szumik C.A. Improvements to resampling measures of group support. Cladistics 2003, 19:324-332.
26. Goloboff P.A., Farris J.S., Nixon K. TNT, a free program for phylogenetic analysis. Cladistics 2008, 24:774-786.
27. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp. Ser. 1999, 41:95-98.
28. Katoh K., Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 2008, 9:286-298.
29. Kores P.J., Weston P.H., Molvray M., Chase M.W. Phylogenetic relationships within the Diurideae (Orchidaceae): inferences from plastid matK DNA sequences. Monocots Systematics and Evolution 2000, 449-456. CSIRO, Melbourne. K.L. Wilson, D.A. Morrison (Eds.).
30. Kores P.J., Molvray M., Weston P.H., Hopper S.D., Brown A., Cameron K.M., Chase M.W. A phylogenetic analysis of Diurideae (Orchidaceae) based on plastid DNA sequence data. Am. J. Bot. 2001, 88:1903-1914.
31. Liu J.-S., Schardl C.L. A conserved sequence in Internal Transcribed Spacer 1 of plant nuclear rRNA genes. Plant Mol. Biol. 1994, 26:775-778.
32. Mayol M., Rosselló J.A. Why nuclear ribosomal DNA spacers (ITS) tell different stories in Quercus. Mol. Phylogenet. Evol. 2001, 19:167-176.
33. Müller K. SeqState - primer design and sequence statistics for phylogenetic DNA data sets. Appl. Bioinform. 2005, 4:65-69.
34. Nieuwenhuizen G.W. Discovery of a surprising orchid in Talca. Gayana Bot. 1993, 50:11-16.
35. Nishimoto Y., Ohnishi O., Hasegawa M. Topological incongruence between nuclear and chloroplast DNA trees suggesting hybridization in the Urophyllum group of the genus Fagopyrum (Polygonaceae). Genes Genet. Syst. 2003, 78:139-153.
36. Novoa P., Espejo J., Cisternas M., Rubio M., Domínguez E. Guía de Campo de las Orquídeas Chilenas 2006, Corporación Chilena de la Madera, Concepción.
37. Posada D., Crandall K.A. ModeltestL testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
38. Pridgeon A., Cribb P.J., Chase M.W., Rasmussen F.N. Genera Orchidacearum, Orchidoideae (Part Two) - Vanilloideae 2003, Oxford University Press, Oxford.
39. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
40. Salazar G.A., Cabrera L.I., Madrinan S., Chase M.W. Phylogenetic relationships of Cranichidinae and Prescottiinae (Orchidaceae, Cranichideae) inferred from plastid and nuclear DNA sequences. Ann. Bot. 2009, 104:403-416.
41. Simmons M.P., Ochotorena H. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 2000, 49:369-381.
42. Soltis D.E., Mavrodiev E.V., Doyle J.J., Rauscher J., Soltis P.S. ITS and ETS sequence data and phylogeny reconstruction in allopolyploids and hybrids. Syst. Bot. 2008, 33:7-20.
43. Syring J., Farrell K., Businsky R., Cronn R., Liston A. Widespread genealogical nonmonophyly in species of Pinus subgenus Strobus. Syst. Biol. 2007, 56:163-181.
44. Szlachetko D.L. Systema orchidalium. Fragm. Florist Geobot. Suppl. 1995, 3:1-152.
45. Szlachetko D.L., Margońska H.B. Genera et species Orchidalium. 4. Pol. Bot. J. 2001, 46:123-125.
46. Szlachetko D.L., Tukałło P. Notes on subtribe Chloraeinae (Orchidaceae). Acta Soc. Bot. Pol. 2008, 77:111-116.
47. Tsutsui K., Suwa A., Sawada K., Kato T., Ohsawa T.A., Watano Y. Incongruence among mitochondrial, chloroplast and nuclear gene trees in Pinus subgenus Strobus (Pinaceae). J. Plant Res. 2009, 122:509-521.
48. Vidal O. Flora de Torres del Paine, Guía de Campo 2008, Fantástico Sur Editorial, Punta Arenas. second ed.