Molecular phylogenetic analysis of Dendrobium (Orchidaceae), with emphasis on the Australian section Dendrocoryne, and implications for generic classification
Jacinta M. Burke A C , Michael J. Bayly A , Peter B. Adams A B and Pauline Y. Ladiges A BA School of Botany, The University of Melbourne, Vic. 3010, Australia.
B Royal Botanic Gardens, Melbourne, Private Bag 2000, South Yarra, Vic. 3141, Australia.
C Corresponding author. Email: j.burke@pgrad.unimelb.edu.au
Australian Systematic Botany 21(1) 1-14 https://doi.org/10.1071/SB07038
Submitted: 16 August 2007 Accepted: 3 December 2007 Published: 3 April 2008
Abstract
Sequences of the internal transcribed spacers (ITS) of nuclear rDNA were obtained for a broad range of dendrobium orchids for phylogenetic analysis using parsimony. A progressive approach was used to identify functional outgroups for analysis of all taxa in Dendrobium sect. Dendrocoryne. Our first, broadest analysis confirmed the results of other workers that Dendrobium sensu lato includes a major Australasian clade and a sister Asian clade. In the Australasian clade, the New Zealand species D. cunninghamii (=gen. Winika, Clements et al. 1997) was identified as the sister group to a well supported clade that includes the genera Cadetia, Diplocaulobium and Flickingeria, and Dendrobium sects Grastidium, Latouria, Spatulata, Australorchis (=gen. Australorchis), Rhizobium (= gen. Dockrillia) and Dendrocoryne. Sect. Dendrocoryne is probably polyphyletic, with two species, D. aemulum and D. callitrophilum (=gen. Tropilis), outside the main group and sect. Rhizobium (= gen. Dockrillia) nested within it. Sect. Australorchis (= gen. Australorchis) is possibly the sister group to the clade of Rhizobium plus the main group of Dendrocoryne. Thelychiton (a genus reinstated for several species in Dendrocoryne) is polyphyletic, given that Tetrabaculum (=D. tetragonum complex) and Dockrillia fall within the same clade. The splitting of the Australasian dendrobiums into various genera by other authors is excessive and unnecessary, and alternative taxonomic treatments are offered here for debate. Our study included accessions for all varieties in the following three widespread eastern Australian species: D. speciosum, D. kingianum and D. tetragonum. Each of these species showed significant sequence divergence between particular geographic regions, but some varieties had identical sequences. The splitting of D. speciosum into 11 species is not supported. We identified pseudogenes in the ITS region for D. fleckeri and D. finniganense, which appear to have evolved before these two species diverged, but support their sister relationship. Sequences for D. callitrophilum and D. (Grastidium) baileyi (the latter from GenBank) also appear to be pseudogenes, and these taxa need further study.
Acknowledgements
We thank J. Bataldo, B. Gray, P. Lavarack, J. Nuss, G. Stocker and D. Williams for supply of some orchid material, and Dr D. Murphy for advice and access to the Molecular Systematics Laboratory, Royal Botanic Gardens, Melbourne. J. B. acknowledges support from the Hansjorg Eichler Scientific Research Fund, the Macbain Research Scholarship and a University of Melbourne Research Scholarship.
Adams PB,
Burke JM, Lawson SD
(2006a) A review of the taxonomy and relationships of the Dendrobium speciosum complex (Orchidaceae), and recognition of two new taxa. Telopea 11, 195–232.
Adams PB,
Burke JM, Lawson SD
(2006b) Systematic analysis of Dendrobium Swartz section Dendrocoryne in the Australian region. Plant Systematics and Evolution 260, 65–80.
| Crossref | GoogleScholarGoogle Scholar |
Adams PB,
Burke JM, Lawson SD
(2006c) Dendrobium speciosum (Dendrocoryne: Orchidaceae) complex in north Queensland. Australian Systematic Botany 19, 259–271.
| Crossref | GoogleScholarGoogle Scholar |
Bailey CD,
Carr TG,
Harris SA, Hughes CE
(2003) Characterization of angiosperm nrDNA polymorphism, paralogy, and pseudogenes. Molecular Phylogenetics and Evolution 29, 435–455.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Bayly MJ, Ladiges PY
(2007) Divergent paralogues of ribosomal DNA in eucalypts. Molecular Phylogenetics and Evolution 44, 346–356.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Bayly MJ,
Udovicic F,
Gibbs AK,
Parra-O. C, Ladiges PY
(2008) Ribosomal DNA pseudogenes are widespread in the eucalypt group (Myrtaceae): implications for phylogenetic analysis. Cladistics ,
Buckler ES,
Ippolito A, Holtsford TP
(1997) The evolution of ribosomal DNA: divergent paralogues and phylogenetic implications. Genetics 145, 821–832.
| PubMed |
Burke JM, Adams PB
(2002) Variation in the Dendrobium speciosum (Orchidaceae) complex: a numerical approach to the species problem. Australian Systematic Botany 15, 63–80.
| Crossref | GoogleScholarGoogle Scholar |
Clements MA
(2003) Molecular phylogenetic systematics in the Dendrobiinae (Orchidaceae), with emphasis on Dendrobium section Pedilonum. Telopea 10, 247–298.
Clements MA
(2006) Molecular phylogenetic systematics in Dendrobieae (Orchidaceae). Aliso 22, 465–480.
Clements MA, Jones DL
(2002) Nomenclatural changes in the Dendrobieae (Orchidaceae). 1: The Australasian region. Orchadian 13, 485–497.
Clements MA,
Jones DL,
Sharma IK,
Knightingale ME,
Garratt MJ,
Fitzgerald KJ,
Mackenzie AM, Malloy BPJ
(2002) Phylogenetics of Diurideae (Orchidaceae) based on the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA. Lindleyana 17, 135–171.
Clements ML,
Jones DL, Molloy BPJ
(1997) Winika, a new monotypic genus for the New Zealand orchid previously known as Dendrobium cunninghamii Lindl. Orchadian 12, 214–219.
Devos N,
Oh S-H,
Raspe O,
Jacquemart A-L, Manos PS
(2005) Nuclear ribosomal DNA sequence variation and evolution of spotted marsh-orchids (Dactylorhiza maculata group). Molecular Phylogenetics and Evolution 36, 568–580.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Douzery EJP,
Pridgeon AM,
Kores P,
Linder HP,
Kurzweil H, Chase MW
(1999) Molecular phylogenetics of Diseae (Orchidaceae): a contribution from nuclear ribosomal ITS sequences. American Journal of Botany 86, 887–899.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Jobes DV, Thien LB
(1997) A conserved motif in the 5.8S ribosomal RNA (rRNA) gene is a useful diagnostic marker for plant internal transcribed spacer (ITS) sequences. Plant Molecular Biology Reporter 15, 326–334.
| Crossref | GoogleScholarGoogle Scholar |
Jones DL,
Clements MA, Sharma I
(2006) Towards a revision of the Thelychiton speciosus group. Australian Orchid Research 5, 34–44.
Kass E, Wink M
(1997) Molecular phylogeny and phylogeography of Lupinus (Leguminosae) inferred from nucleotide sequences of the rbcL gene and ITS1 + 2 regions of rDNA. Plant Systematics and Evolution 208, 139–167.
| Crossref | GoogleScholarGoogle Scholar |
Koehler S,
Williams NH,
Whitten WM, do Amaral Md CE
(2002) Phylogeny of the Bifrenaria (Orchidaceae) complex based on morphology and sequence data from nuclear rDNA internal transcribed spacers (ITS) and chloroplast trnL–trnF region. International Journal of Plant Sciences 163, 1055–1066.
| Crossref | GoogleScholarGoogle Scholar |
Lindley J
(1844) Dendrobium. Botanical Register 30, 46–64.
Lindley J, Paxton J
(1851) The transparent dendrobe. Paxton’s Flower Garden 1, 133–136.
Liston A,
Robinson WA,
Oliphant JM, Alvarez-Buylla ER
(1996) Length variation in the nuclear ribosomal DNA internal transcribed spacer region of non-flowering seed plants. Systematic Botany 21, 109–120.
| Crossref | GoogleScholarGoogle Scholar |
Liu JS, Schardl CL
(1994) A conserved sequence in internal transcribed spacer 1 of plant nuclear rRNA genes. Plant Molecular Biology 26, 775–778.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Mayol M, Roselló JA
(2001) Why nuclear ribosomal spacers (ITS) tell different stories in Quercus. Molecular Phylogenetics and Evolution 19, 167–176.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Pridgeon AM,
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.
| Crossref | GoogleScholarGoogle Scholar |
Razafimandimbison SG,
Kellogg EA, Bremer B
(2004) Recent origin and phylogenetic utility of divergent ITS putative pseudogenes: a case study from Naucleeae (Rubiaceae). Systematic Biology 53, 177–192.
| Crossref |
PubMed |
Rosner B
(1983) Percentage points for a generalized ESD many-outlier procedure. Technometrics 25, 165–172.
| Crossref | GoogleScholarGoogle Scholar |
Sanderson MJ, Doyle JJ
(1992) Reconstruction of organismal and gene phylogenies from data on multigene families: concerted evolution, homoplasy, and confidence. Systematic Biology 41, 4–17.
| Crossref | GoogleScholarGoogle Scholar |
Schluter PM,
Kohl G,
Stuessy TF, Paulus HF
(2007) A screen of low copy genes reveals the LFY gene as phylogenetically informative in closely related species of orchids (Ophrys). Taxon 56, 493–504.
Sun Y,
Skinner DZ,
Liang GH, Hulbert SH
(1994) Phylogenetic analysis of Sorghum and related taxa using internal transcribed spacers of nuclear ribosomal DNA. Theoretical and Applied Genetics 89, 26–32.
| Crossref | GoogleScholarGoogle Scholar |
van den Berg C,
Ryan A,
Cribb PJ, Chase MW
(2002) Molecular phylogenetics of Cymbidium (Orchidaceae: Maxillarieae): sequence data from internal transcribed spacers (ITS) of nuclear ribosomal DNA and plastid matK. Lindleyana 17, 102–111.
van den Berg C,
Goldman DH,
Freudenstein JV,
Pridgeon AM,
Cameron KM, Chase MW
(2005) An overview of the phylogenetic relationships within Epidendroideae inferred from multiple DNA regions and recircumscription of Epidendreae and Arethuseae (Orchidaceae). American Journal of Botany 92, 613–624.
| Crossref |
Whitten WM,
Williams NH, Chase MW
(2000) Subtribal and generic relationships of Maxillarieae (Orchidaceae) with emphasis of Stanhopeinae: combined molecular evidence. American Journal of Botany 87, 1842–1856.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Yukawa T, Uehara K
(1996) Vegetative diversification and radiation in subtribe Dendrobiinae (Orchidaceae): evidence from chloroplast DNA phylogeny and anatomical characters. Plant Systematics and Evolution 201, 1–14.
| Crossref | GoogleScholarGoogle Scholar |
Yukawa T,
Kurita S,
Nishida M, Hasebe M
(1993) Phylogenetic implications of chloroplast DNA restriction site variation in subtribe Dendrobiinae (Orchidacaeae). Lindleyana 8, 211–221.
Yukawa T,
Ohba H,
Cameron KM, Chase MW
(1996) Choloroplast DNA phylogeny of subtribe Dendrobiinae (Orchidaceae): insights from a combined analysis based on rbcL sequences and restriction site variation. Journal of Plant Research 109, 169–176.
| Crossref | GoogleScholarGoogle Scholar |
Zuker M
(2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research 31, 3406–3415.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
