Free Standard AU & NZ Shipping For All Book Orders Over $80!
Register      Login
Australian Systematic Botany Australian Systematic Botany Society
Taxonomy, biogeography and evolution of plants
Shopping Cart: ( empty )
You are here: Home > Journals > SB > SB08029
RESEARCH ARTICLE
Contents Vol 22(1)

A molecular phylogenetic analysis of Diuris (Orchidaceae) based on AFLP and ITS reveals three major clades and a basal species

James O. Indsto A C D , Peter H. Weston A and Mark A. Clements B
+ Author Affiliations
- Author Affiliations

A National Herbarium of NSW, Mrs Macquaries Road, Sydney, NSW 2000, Australia.

B Centre for Plant Biodiversity Research, National Botanic Gardens, Canberra, ACT 2601, Australia.

C Institute for Conservation Biology, University of Wollongong, NSW 2522, Australia. Present address: Forensic Science Services Branch, Forensic Services Group, NSW Police Force.

D Corresponding author. Email: inds1jam@police.nsw.gov.au

Australian Systematic Botany 22(1) 1-15 https://doi.org/10.1071/SB08029
Submitted: 17 June 2008  Accepted: 24 November 2008   Published: 11 March 2009

Abstract

Diuris is a terrestrial orchid genus of at least 61 and possibly more than 100 species, restricted to Australia except for one species endemic in Timor. Distinctive species groups have respective eastern and western centres of distribution. Although species affinities have been vaguely understood for many years, no formal infrageneric treatment has been undertaken as Diuris possesses few reliable morphological characters for a classification system. We have undertaken cladistic parsimony and Bayesian phylogenetic analyses of Diuris by using the ITS1–5.8S–ITS2 region of nuclear rDNA and morphological characters, with a subset of samples also studied by amplified fragment length polymorphism (AFLP) as an independent test of phylogenetic relationships. Four major clades with strong bootstrap support were resolved and are named here according to a recently published classification; D. sulphurea forms a lineage (subg. Paradiuris) of its own that is well supported as the sister to the rest of Diuris. Two other major eastern clades contained species related to D. maculata (subg. Xanthodiuris) and D. punctata (subg. Diuris), respectively. Although these latter two subgenera are genetically well resolved, there is minimal genetic variation at species level, consistent with recent, rapid speciation. A fourth clade (subg. Hesperodiuris) has a centre of distribution in Western Australia, and has more genetic and morphological variation than the eastern subgenera. Total evidence analysis provides support for the western clade being sister group to the two eastern subgenera Diuris and Xanthodiuris; however, this relationship was not resolved by molecular data. Hybridisation is known to be common among species within subgenera Diuris and Xanthodiuris. Instances of incongruence between different datasets were found suggestive of hybridisation events between species of different sections of Diuris.


Acknowledgements

This work has been undertaken as part completion of a Master of Science degree by JI. Financial support for the project was from a Hermon Slade Orchid Trust grant. The Westmead Millennium Institute (University of Sydney) kindly provided laboratory facilities. John Riley in particular gave much advice on Diuris colony locations and flowering times. Michael Batley provided several Diuris samples used in this study. We also thank Debby McGerty for editing of graphics.


References


Beardsell DV, Clements MA, Huthchinson JF, Williams EG (1986) Pollination of Diuris maculata R.Br. (Orchidaceae) by floral mimicry of the native legumes Daviesia spp. and Pultenaea scabra R.Br. Australian Journal of Botany 34, 165–174.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Clements MA (2003) Molecular phylogenetic systematics in the Dendrobiinae (Orchidaceae), with emphasis on Dendrobium section Pedilonum. Telopea 10, 247–298. open url image1

Clements MA, Jones DL, Sharma I, Nightingale ME, Garratt MJ, Fitzgerald KJ, MacKenzie AM, Molloy BPJ (2002) Phylogenetics of Diurideae (Orchidaceae) based on the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA. Lindleyana 17, 135–171. open url image1

Cox A, 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.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Coyle HM, Palmbach T, Juliano N, Ladd C, Lee HC (2003) An overview of DNA methods for the identification and individualization of marijuana. Croatian Medical Journal 44, 315–321.
| PubMed |
open url image1

Dressler R (1990) ‘The orchids: natural history and classification.’ (Harvard University Press: Cambridge, MA)

Engel MS (2000) A new interpretation of the oldest fossil bee (Hymenoptera: Apidae). American Museum Novitates 3296, 1–11.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Farris J (1969) A successive approximations approach to character weighting. Systematic Zoology 18, 374–385.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Giambernardi TA, Rodeck U, Klebe RJ (1998) Bovine serum albumin reverses inhibition of RT–PCR by melanin. BioTechniques 25, 564–566.
|  CAS | PubMed |
open url image1

Gould SJ , Eldredge N (1972) Punctuated equilibria: an alternative to phyletic gradualism. In ‘Models in paleobiology’. (Ed. TJM Schopf) pp. 82–115. (Freeman, Cooper and Co.: San Francisco)

Gravendeel B, Chase MW, de Vogel EF, Roos MC, Mes THM, Bachman 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.
| Crossref | GoogleScholarGoogle Scholar | CAS | open url image1

Hedren M, Fay MF, Chase MW (2001) Amplified fragment length polymorphisms (AFLP) reveal details of polyploid evolution in Dactylorhiza (Orchidaceae). American Journal of Botany 88, 1868–1880.
| Crossref | GoogleScholarGoogle Scholar | CAS | open url image1

Indsto JO, Weston PH, Clements MA, Whelan RJ (2005) Highly sensitive DNA fingerprinting of orchid pollinaria remnants using AFLP. Australian Systematic Botany 18, 207–213.
| Crossref | GoogleScholarGoogle Scholar | CAS | open url image1

Indsto JO, Weston PH, Clements MA, Dyer AG, Batley M, Whelan RJ (2006) Pollination of Diuris maculata R.Br. (Orchidaceae) in the Sydney region, NSW by male Trichocolletes venustus bees. Australian Journal of Botany 54, 669–679.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Indsto J, Weston PH, Clements MA, Dyer AG, Batley M, Whelan RJ (2007) Generalised pollination of Diuris alba (Orchidaceae) by small bees and wasps. Australian Journal of Botany 55, 628–634.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Jones D (2000) ‘Natural groups in Diuris Sm.’ Fourth Australasian native orchid conference and show, Karralyka Centre, Melbourne. (Australasian Native Orchid Society)

Jones D (2006) ‘Complete guide to native orchids in Australia: including the Island Territories.’ (New Holland Publishers Australia: Frenchs Forest)

Jones D, Clements MA (2006) The infrageneric classification of Diuris Smith (Orchidaceae). The Orchadian 15, 203–206. open url image1

Keith D (2004) ‘Ocean shores to desert dunes: the native vegetation of New South Wales and the ACT.’ (NSW Department of Environment and Conservation: Sydney)

Kores PJ, Molvray M, Weston PH, Hopper SD, Brown AP, Cameron KM, Chase MW (2001) A phylogenetic analysis of Diurideae (Orchidaceae) based on plastid DNA sequence data. American Journal of Botany 88, 1903–1914.
| Crossref | GoogleScholarGoogle Scholar | CAS | open url image1

Krauss SL (2000) Patterns of mating in Persoonia mollis (Proteaceae) revealed by an analysis of paternity using AFLP: implications for conservation. Australian Journal of Botany 48, 349–356.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Lewis PO (2001) A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology 50, 913–925.
| Crossref | GoogleScholarGoogle Scholar | CAS | PubMed | open url image1

Mant J, Peakall R, Weston PH (2005) Specific pollinator attraction and the diversification of sexually deceptive Chiloglottis (Orchidaceae). Plant Systematics and Evolution 253, 185–200.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Michener CD, Grimaldi DA (1988) The oldest fossil bee: apoid history evolutionary stasis, and antiquity of social behavior. Proceedings of the National Academy of Sciences, USA 85, 6424–6426.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Okuyama Y, Noriyuki F, Wakabayashi M, Kawakita A, Ito M, Watanabe M, Murakami N, Kato M (2004) Nonuniform concerted evolution and chloroplast capture capture:heterogeneity of observed introgression patterns in three molecular data partition phylogenies of Asian Mitella (Saxifagaceae). Molecular Biology and Evolution 22, 285–296.
| Crossref | GoogleScholarGoogle Scholar | PubMed | open url image1

Orthia L, Crisp MD, Cook LG, de Kok RPJ (2005) Bush peas: a rapid radiation with no support for monophyly of Pultenaea (Fabaceae: Mirbeliae). Australian Journal of Botany 18, 133–147.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Pridgeon A, Solano R, Chase MW (2001) Phylogenetic relationships in Pleurothallidinae (Orchidaceae): combined evidence from nuclear and plastid sequences. American Journal of Botany 88, 2286–2308.
| Crossref | GoogleScholarGoogle Scholar | CAS | open url image1

Ramirez S, Gravendeel B, Singer RB, Marshall CR, Pierce NE (2007) Dating the origin of the Orchidaceae from a fossil record record with its pollinator. Nature 448, 1042–1045.
| Crossref | GoogleScholarGoogle Scholar | CAS | PubMed | open url image1

Ranamukhaarachchi DG, Kane ME, Guy CL, Li QB (2000) Modified AFLP technique for rapid genetic characterization in plants. BioTechniques 29, 858–866.
|  CAS | PubMed |
open url image1

Simmons MP, Ochoterena H (2000) Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology 49, 369–381.
| Crossref | GoogleScholarGoogle Scholar | CAS | PubMed | open url image1

Sun Y, Skinner DZ, Liang GM, Hubert 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 | CAS | open url image1

Swofford DL (2003) ‘PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4.’ (Sinauer Associates: Sunderland, MA)

van der Cingel N (2001) ‘An atlas of orchid pollination: America, Africa, Asia and Australia.’ (AA Balkema Publishers: Rotterdam, The Netherlands)

Vos P, Hogers R, Bleeker M, Reijans M, van der Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research 23, 4407–4414.
| Crossref | GoogleScholarGoogle Scholar | CAS | PubMed | open url image1

Weider LJ, Elser JJ, Crease TJ, Mateos M, Cotner JB, Markow TA (2005) The functional significance of ribosomal (rDNA) variation: impacts on the evolutionary ecology of organisms. Annual Review of Ecology and Systematics 36, 219–242.
| Crossref | GoogleScholarGoogle Scholar | open url image1

Wojciechowski M (2003) Reconstructing the phylogeny of legumes (Leguminosae): an early 21st century perspective. In ‘Advances in legume systematics’. Part 10. Higher level systematics. (Eds B Klitgaard, A Bruneau) pp. 5–35. (Royal Botanic Gardens, Kew: London)









Appendix 1.  Diuris species list compiled by Mark Clements, current as at December 2008 (see http://anbg.gov.au/cpbr/cd-keys/orchidkey/html/currentspecies.html)

Diuris Sm., Trans. Linn. Soc. London 4: 222 (1798). Type species: Diuris aurea Sm.

subgen. Diuris

Sect. Diuris

Synonym: Diuris sect. Flaviflorae G.Don in Loudon’s Hortus Britannicus 368 (1830). Type species: Diuris aurea Sm., fide Jones and Clements (2006).

Diuris aurea Smith, Exotic Bot. 1: 15, t. 9 (1805).

Diuris byronensis D.L.Jones, Orchadian 14(3): 132–133, f. 1, t. (2003).

Diuris chrysantha D.L.Jones et M.A.Clem., Proc. Roy. Soc. Queensland 98: 130–132, f. 7 (1987).

Diuris disposita D.L.Jones, Austral. Orch. Res. 2: 55, f. 69 (1991).

Diuris flavescens D.L.Jones, Austral. Orch. Res. 2: 56, f. 71 (1991).

Diuris luteola D.L.Jones et B.Gray, Austral. Orch. Res. 2: 57–58, f. 73 (1991).

Diuris unica D.L.Jones, Austral. Orch. Res. 5: 82, f. 3.13, t. (21 Dec. 2006).

Diuris secundiflora Fitzg., Austral. Orch. 1(4): [t. 9] (1878).

Diuris tricolor Fitzg., J. Bot. 23: 137 (1885).

sect. Purpureo-albae G.Don in Loudon’s Hortus Britannicus 368 (1830). Type species: Diuris alba R.Br., fide Jones and Clements (2006).

Diuris alba R.Br., Prod. 326 (1810).

Diuris arenaria D.L.Jones, Orchadian 12(12): 567–568, f. 1, t. (1999).

Diuris callitrophila D.L.Jones, Orchadian 14(3): 133–135 (2003).

Diuris curta D.L.Jones, Austral. Orchid. Res. 5: 76–77, f. 3.9 (21 Dec. 2006).

Diuris daltonii (C.Walter) D.L.Jones et M.A.Clem., Orchadian 14(8): Sci. Suppl. xiv (June 2004).

Diuris dendrobioides Fitzg., Austral. Orch. 1(7): [t. 3] (1882).

Diuris fragrantissima D.L.Jones et M.A.Clem., Austral. Orch. Res. 1: 68 (1989).

Diuris minor (Benth.) D.L.Jones et M.A.Clem., Orchadian 14(8): Sci. Suppl. xiv (June 2004).

Diuris oporina D.L.Jones, Austral. Orch. Res. 2: 59–60, f. 77 (1991).

Diuris parvipetala (Dockrill) D.L.Jones et M.A.Clem., Proc. Roy. Soc. Queensland 98: 132 (1987).

Diuris punctata Sm. var. punctata Exotic Bot. 1: 13, t. 8 (1804).

Diuris punctata Sm. var. sulphurea Rupp, Proc. Linn. Soc. New South Wales 69: 73 (1944).

subgen. Xanthodiuris D.L.Jones et M.A.Clem., Orchadian 15(5): 203 (2006). Type species: Diuris maculata Sm.

sect. Xanthodiuris

Diuris aequalis F.Muell. ex Fitzg., Austral. Orch. 1(2): [t. 6] (1876).

Diuris bracteata Fitzg., Austral. Orch. 2(4): [t. 2] (1889).

Diuris cuneilabris Rupp, Proc. Linn. Soc. New South Wales 73: 134, f. 1 (1948).

Diuris goonooensis Rupp, Victorian Naturalist 72: 110 (1955).

Diuris maculata Sm., Exotic Bot. 1: 57, t. 30 (1804–05).

Diuris nigromontana D.L.Jones, Orchadian 15(12): 550–551, t. (June 2008).

Diuris pardina Lindl., Gen. sp. orchid. pl. 507 (1840).

Diuris platichila Fitzg., Austral. Orch. 2(4): [t. 3] (1891).

Diuris semilunulata Messmer in Rupp, Orch. New South Wales 139–140 (1943).

sect. Abbreviatae D.L.Jones et M.A.Clem., Orchadian 15(5): 203–204 (2006). Type species: Diuris abbreviata Benth.

Diuris abbreviata Benth., Fl. Austral. 6: 329 (1873).

Diuris exitela D.L.Jones, Austral. Orch. Res. 2: 55–56, f. 70 (1991).

Diuris praecox D.L.Jones, Austral. Orch. Res. 2: 60, f. 78 (1991).

sect. Pedunculatae D.L.Jones et M.A.Clem., Orchadian 15(5): 204 (2006). Type species: Diuris pedunculata R.Br.

Diuris basaltica D.L.Jones, Austral. Orch. Res. 5: 75–76, f. 3.9 (21 Dec. 2006).

Diuris behrii Schldl., Linnaea 20: 572 (1849).

Diuris chryseopsis D.L.Jones, Austral. Orch. Res. 3: 74–75, f. 4.1 (1998).

Diuris eborensis D.L.Jones, Austral. Orch. Res. 5: 77–78, f. 3.10, t. (21 Dec. 2006).

Diuris fucosa D.L.Jones, Austral. Orch. Res. 5: 78, f. 3.11, t. (21 Dec. 2006).

Diuris gregaria D.L.Jones, Austral. Orch. Res. 5: 79–80, f. 3.12 (21 Dec. 2006).

Diuris lanceolata Lindl., Gen. sp. orchid. pl. 508 (1840).

Diuris monticola D.L.Jones, Austral. Orch. Res. 3: 76–77, f. 4.3 (1998).

Diuris ochroma D.L.Jones, Muelleria 8(2): 182–184, f. 2 d-f (1994).

Diuris pedunculata R.Br., Prod. 316 (1810).

Diuris protena D.L.Jones, Austral. Orch. Res. 5: 81–82 (21 Dec. 2006).

Diuris subalpina D.L.Jones, Orchadian 15(12): 551, t. (June 2008).

Diuris venosa Rupp, Proc. Linn. Soc. New South Wales 51: 313, f. 1–6 (1926).

subgen. Hesperodiuris D.L.Jones et M.A.Clem., Orchadian 15(5): 204 (2006). Type species: Diuris laxiflora Lindl.

sect. Hesperodiuris

Synonym: Diuris subgen. Hesperodiuris sect. Setaceae D.L.Jones et M.A.Clem., Orchadian 15(5): 204 (2006). Type species: Diuris setacea R.Br.

Diuris brevifolia R.S.Rogers, Trans. & Proc. Roy. Soc. South Australia 46: 148 (1922).

Diuris carinata Lindl., Gen. sp. orchid. pl. 510 (Sep. 1840).

Diuris concinna D.L.Jones, Austral. Orch. Res. 2: 53–54, f. 67 (1991).

Diuris drummondii Lindl. in Edwards’s, Bot. Reg. 1–23: Swan Riv. Append. li (1840).

Diuris emarginata R.Br., Prod. 316 (1810).

Diuris filifolia Lindl. in Edwards’s, Bot. Reg. 1–23: Swan Riv. Append. li (1840).

Diuris heberlei D.L.Jones, Austral. Orch. Res. 2: 56–576, f. 72 (1991).

Diuris immaculata D.L.Jones, Austral. Orch. Res. 5: 80–81 (21 Dec. 2006).

Diuris laxiflora Lindl. in Edwards’s, Bot. Reg. 1–23: Swan Riv. Append li (1840).D.

Diuris micrantha D.L.Jones, Austral. Orch. Res. 2: 58–59, f. 75 (1991).

Diuris pauciflora R.Br., Prod. 316 (1810).

Diuris picta J.Drummond in Hooker’s, J. Bot. 5: 347 (1853).

Diuris setacea R.Br., Prod. 316 (1810).

sect. Pyrophilae D.L.Jones et M.A.Clem., Orchadian 15(5): 204 (2006). Type species: Diuris laevis Fitzg.

Diuris laevis Fitzg., Gard. Chron. (new ser.), 17: 495 (1882).

Diuris purdiei Diels, J. Proc. Mueller Bot. Soc. Western Australia_1(11): 79 (1903).

sect. Palustres D.L.Jones et M.A.Clem., Orchadian 15(5): 204–205 (2006). Type species: Diuris palustris Lindl.

Diuris palustris Lindl., Gen. sp. orchid. pl. 507 (1840).

sect. Suffusae D.L.Jones et M.A.Clem., Orchadian 15(5): 205 (2006). Type species: Diuris longifolia R.Br.

Diuris amplissima D.L.Jones, Austral. Orch. Res. 2: 53–54, f. 65 (1991).

Diuris brumalis D.L.Jones, Austral. Orch. Res. 2: 53, f. 66 (1991).

Diuris conspicillata D.L.Jones, Austral. Orch. Res. 2: 54–55, f. 68 (1991).

Diuris corymbosa Lindl. in Edwards’s, Bot. Reg. 1–23: Swan Riv. Append. li (1840).

Diuris longifolia R.Br., Prod. 316 (1810).

Diuris magnifica D.L.Jones, Austral. Orch. Res. 2: 58, f. 74 (1991).

Diuris orientis D.L.Jones, Austral. Orch. Res. 3: 77–78, f. 4.4 (1998).

Diuris porrifolia Lindl. in Edwards’s, Bot. Reg. 1–23: Swan. Riv. Append. li (1840).

Diuris pulchella D.L.Jones, Austral. Orch. Res. 2: 61, f. 79 (1991).

Diuris recurva D.L.Jones, Austral. Orch. Res. 2: 61–62, f. 80 (1991).

subgen. Paradiuris D.L.Jones et M.A.Clem., Orchadian 15(5): 205 (2006). Type species: Diuris sulphurea R.Br.

Diuris sulphurea R.Br., Prod. 316 (1810).

subgen. Timordiuris D.L.Jones et M.A.Clem., Orchadian 15(5): 205 (2006). Type species: Diuris fryana Ridl.

Diuris fryana Ridl. in H.O.Forbes, Nat. Wand. East. Archip. 519 (1885).

Natural hybrids

Diuris × fastidiosa R.S.Rogers, Trans. & Proc. Roy. Soc. South Australia 51: 6–7 (1927).

Diuris × nebulosa D.L.Jones, Austral. Orch. Res. 2: 59, f. 76 (1991).

Diuris × palachila R.S. Rogers, Trans. & Proc. Roy. Soc. South Australia 31: 209–210 (1907).

Diuris × polymorpha Messmer in Rupp, Orchids New South Wales, Suppl. 142 (1943).