On the value of nuclear and mitochondrial gene sequences for reconstructing the phylogeny of vanilloid orchids (Vanilloideae, Orchidaceae)

Annals of Botany

Volumn 104, Issue 3, 2009, Pages 377-385

  Cameron, Kenneth M ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

18S rDNA; 26S rDNA; 5 8S rDNA; AtpA; Nad1; Orchids; Plastid; Vanilla; Vanilloid orchids; Vanilloideae

Indexed keywords

DIVERGENCE; GENETIC STRUCTURE; MITOCHONDRIAL DNA; MONOCOTYLEDON; PHYLOGENY; PLASTID; RECONSTRUCTION; TAXONOMY;

ARTICLE; CELL NUCLEUS; CLASSIFICATION; GENETICS; INTRON; MITOCHONDRIAL GENE; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT GENE; RIBOSOME; VANILLA;

BASE SEQUENCE; CELL NUCLEUS; GENES, MITOCHONDRIAL; GENES, PLANT; INTRONS; PHYLOGENY; RIBOSOMES; VANILLA;

LECANORCHIS; ORCHIDACEAE;

EID: 68849088168     PISSN: 03057364     EISSN: 10958290     Source Type: Journal    
DOI: 10.1093/aob/mcp024     Document Type: Article

References (28)

1. Adams KL, Qiu YL, Stoutemyer M, Palmer JD. 2002. Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. Proceedings of the National Acadamy of Sciences, USA 99: 9905-9912.
2. Bult C, Kallersjo M, Suh Y. 1992. Amplification and sequencing of 16/18S rDNA from gel-purified total plant DNA. Plant Molecular Biology Reporter 10: 273-284.
3. Cameron KM. 2003. Vanilloideae. In: Pridgeon A, Cribb P, Chase M, Rasmussen F, eds. Genera orchidacearum vol 3. Oxford: Oxford University Press, 281-334.
4. Cameron KM. 2004. Utility of plastid psaB gene sequences for investigating intrafamilial relationships within Orchidaceae. Molecular Phylogenetics and Evolution 31: 1157-1180.
5. Cameron KM. 2006. A comparison of plastid atpB and rbcL gene sequences for inferring phylogenetic relationships within Orchidaceae. Aliso 22: 447-464.
6. Cameron KM, Chase MW. 1999. Phylogenetic relationships of Pogoniinae (Vanilloideae, Orchidaceae): an herbaceous example of the eastern North America-eastern Asia phytogeographic disjunction. Journal of Plant Research 112: 317-329.
7. Cameron KM, Chase MW. 2000. Nuclear 18S rDNA sequences of Orchidaceae confirm the subfamilial status and circumscription of Vanilloideae. In: Wilson KL, Morrison DA, eds. Monocots, systematics and evolution. Collingwood: CSIRO, 457-464.
8. Cameron KM, Molina MC. 2006. Photosystem II gene sequences of psbB and psbC clarify the phylogenetic position of Vanilla (Vanilloideae, Orchidaceae). Cladistics 22: 239-248.
9. Cameron K, Chase M, Whitten M, et al. 1999. A phylogenetic analysis of the Orchidaceae, evidence from rbcL nucleotide sequences. American Journal of Botany 86: 208-224.
10. Chang CC, Lin HC, Lin IP, et al. 2005. The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications. Molecular Biology and Evolution 23: 279-291.
11. Cox AV, Pridgeon AM, Albert VA, Chase MW. 1997. Phylogenetics of the slipper orchids (Cypripedioideae, Orchidaceae): nuclear rDNA ITS sequences. Plant Systematics and Evolution 208: 197-223.
12. Davis JI, Simmons MP, Stevenson DW, Wendel JF. 1998. Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from monocotyledons using mitochondrial atpA sequences. Systematic Biology 47: 282-310
13. Demesure B, Sodzi N, Petit RJ. 1995. A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants. Molecular Ecology 4: 129-131.
14. Dueck LA, Cameron KM. 2007. Sequencing re-defines Spiranthes relationships, with implications for rare and endangered taxa. Lankesteriana 7: 190-195.
15. Freudenstein JV, Chase MW. 2001. Analysis of mitochondrial nad1b-c intron sequences in Orchidaceae: utility and coding of length-change characters. Systematic Botany 26: 643-657.
16. Goldman D, Freudenstein J, Kores P, et al. 2001. Phylogenetics of Arethuseae (Orchidaceae) based on plastid matK and rbcL sequences. Systematic Botany 26: 670-695.
17. Gravendeel B, ChaseMW, deVogel EF, Roos MC, Mes THM, Bachmann K. 2001. Molecular phylogeny of Coelogyne (Epidendroideae; Orchidaceae) based on plastid RFLPs, matK, and nuclear ribosomal ITS sequences: evidence for polyphyly. American Journal of Botany 88: 1915-1927.
18. Kores PJ, Molvray M, Weston PH, et al. 2001. A phylogenetic analysis of Diurideae (Orchidaceae) based on plastid DNA sequence data. American Journal of Botany 88: 1903-1914.
19. Kuzoff RK, Sweere JA, Soltis DE, Soltis PS, Zimmer EA. 1998. The phylogenetic potential of entire 26S rDNA sequences in plants. Molecular Biology and Evolution 15: 251-263.
20. Linnaeus C. 1753. Species plantarum. 2 vols. Stockholm: L. Salvii. (Facsim. ed. 1957-1959, London.)
21. Molvray M, Kores PJ, Chase MW. 2000. Polyphyly of mycoheterotrophic orchids and functional influences on floral and molecular characters. In: Wilson KL, Morrison DA eds. Monocots: systematics and evolution. Collingwood: CSIRO, 441-448.Neyland R, Urbatsch L. 1996. Evolution in the number and position of fertile anthers in Orchidaceae inferred from ndhF chloroplast gene sequences. Lindleyana 11: 47-53.
22. Nickrent DL, Schuette KP, Starr EM. 1994. A molecular phylogeny of Arceuthobium based upon rDNA internal transcribed spacer sequences. American Journal of Botany 81: 1149-1160.
23. Palmer JD, Adams KL, Cho Y, Parkinson CL, Song K. 2000. Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates. Proceedings of the National Acadamy of Sciences, USA 97: 6960-6966.
24. Petersen G, Seberg O, Davis JI, et al. 2006. Mitochondrial data in monocot phylogenetics. Aliso 22: 52-62.
25. Pridgeon A, Solano R, Chase MW. 2001. Phylogenetic relationships in Pleurothallidinae (Orchidaceae): combined evidence from nuclear and plastid DNA sequences. American Journal of Botany 88: 2286-2308.
26. Ramirez SR, Gravendeel B, Singer RB, Marshall CR, Pierce NE. 2007. Dating the origin of the Orchidaceae from a fossil orchid with its pollinator. Nature 448: 1042-1045.
27. Smith SD, Cowan RS, Gregg KB, Chase MW, Maxted N, Fay MF. 2004. Genetic discontinuities among populations of Cleistes in North America (Orchidaceae, Vanilloideae). Botanical Journal of the Linnean Society 147: 87-95.
28. Swofford DL. 2002. PAUP* 4.0b10, Phylogenetic analysis using parsimony (* and other methods). Sunderland, MA: Sinauer Associates.