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Australian Systematic Botany Australian Systematic Botany Society
Taxonomy, biogeography and evolution of plants
RESEARCH ARTICLE

An expanded phylogenetic analysis of Austrostipa (Poaceae: Stipeae) to test infrageneric relationships

Anna E. Syme A C , Daniel J. Murphy A , Gareth D. Holmes B , Stuart Gardner A , Rachael Fowler A and David J. Cantrill A
+ Author Affiliations
- Author Affiliations

A National Herbarium of Victoria, Royal Botanic Gardens Melbourne, Vic. 3141, Australia.

B Current address: Landcare Research, PO Box 40, Lincoln 7640, New Zealand.

C Corresponding author. Email: anna.syme@rbg.vic.gov.au

Australian Systematic Botany 25(1) 1-10 https://doi.org/10.1071/SB10049
Submitted: 26 November 2010  Accepted: 6 October 2011   Published: 9 March 2012

Abstract

Although the Australasian grass genus Austrostipa is species rich, abundant and ecologically significant, the subgeneric classification of its 62 species has not been comprehensively tested with molecular data. We used three molecular markers from 51 species to determine a phylogeny of the genus and found strong support for the following seven of the existing subgenera: Falcatae, Austrostipa, Aulax, Lobatae, Bambusina, Lancea and Longiaristatae. The molecular data do not support Tuberculatae and Eremophilae, which could be combined with subgenus Austrostipa. The data are equivocal or insufficient regarding monophyly of Ceres, Arbuscula, Petaurista and Lanterna. Data from the nuclear internal transcribed spacer region appear to be suitable for phylogenetic analysis of this group, and the degree of sequence variability resolves species-level relationships with good levels of support. In contrast, chloroplast sequence data from the matK and rbcL genes do not resolve most relationships at the species level, and the inferred phylogeny hints at gene duplication, chloroplast capture, or deep coalescence in the evolutionary history of Austrostipa.

Additional keywords: Australian grasses, ITS, matK, molecular phylogeny, rbcL.


References

Baker KS, Steadman KJ, Plummer JA, Dixon KW (2005) Seed dormancy and germination responses of nine Australian fire ephemerals. Plant and Soil 277, 345–358.
Seed dormancy and germination responses of nine Australian fire ephemerals.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2MXht1GlsLrF&md5=7d7c79fd9cbb2fd7c46f0094845498b1CAS |

Barber JC, Finch CC, Francisco-Ortega J, Santos-Guerra A, Jansen RK (2007) Hybridization in Macaronesian Sideritis (Lamiaceae): evidence from incongruence of multiple independent nuclear and chloroplast sequence datasets. Taxon 56, 74–88.

Barber JC, Hames KA, Cialdella AM, Giussani LM, Morrone O (2009) Phylogenetic relationships of Piptochaetium Presl (Poaceae: Stipeae) and related genera reconstructed from nuclear and chloroplast sequence datasets. Taxon 58, 375–380.

Barkworth ME, Arriaga MO, Smith JF, Jacobs SWL, Valdes-Reyna J, Bushman BS (2008) Molecules and morphology in South American Stipeae (Poaceae). Systematic Botany 33, 719–731.
Molecules and morphology in South American Stipeae (Poaceae).Crossref | GoogleScholarGoogle Scholar |

Bentley AR, Petrovic T, Griffiths SP, Burgess LW, Summerell BA (2007) Crop pathogens and other Fusarium species associated with Austrostipa aristiglumis. Australasian Plant Pathology 36, 434–438.
Crop pathogens and other Fusarium species associated with Austrostipa aristiglumis.Crossref | GoogleScholarGoogle Scholar |

Bouchenak-Khelladi Y, Salamin N, Savolainen V, Forest F, van der Bank M, Chase MW, Hodkinson TR (2008) Large multi-gene phylogenetic trees of the grasses (Poaceae): Progress towards complete tribal and generic level sampling. Molecular Phylogenetics and Evolution 47, 488–505.
Large multi-gene phylogenetic trees of the grasses (Poaceae): Progress towards complete tribal and generic level sampling.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXlslKlu7o%3D&md5=8d3bd465e28cba183be50fbc2c95404cCAS |

Bustam BM (2010) Systematic studies of Australian stipoid grasses (Austrostipa) based on micro-morphological and molecular characteristics. Biodiversitas 11, 9–14.

Cialdella AM, Giussani LM, Aagesen L, Zuloaga FO, Morrone O (2007) A phylogeny of Piptochaetium (Poaceae: Pooideae: Stipeae) and related genera based on a combined analysis including trnL-F, rp116, and morphology. Systematic Botany 32, 545–559.
A phylogeny of Piptochaetium (Poaceae: Pooideae: Stipeae) and related genera based on a combined analysis including trnL-F, rp116, and morphology.Crossref | GoogleScholarGoogle Scholar |

Cialdella AM, Salariato DL, Aagesen L, Giussani LM, Zuloaga FO, Morrone O (2010) Phylogeny of New World Stipeae (Poaceae): an evaluation of the monophyly of Aciachne and Amelichloa. Cladistics 26, 563–578.
Phylogeny of New World Stipeae (Poaceae): an evaluation of the monophyly of Aciachne and Amelichloa.Crossref | GoogleScholarGoogle Scholar |

Commander LE, Merritt DJ, Rokich DP, Dixon KW (2009) Seed biology of Australian arid zone species: germination of 18 species used for rehabilitation. Journal of Arid Environments 73, 617–625.
Seed biology of Australian arid zone species: germination of 18 species used for rehabilitation.Crossref | GoogleScholarGoogle Scholar |

Cummings MP, Nugent JM, Olmstead RG, Palmer JD (2003) Phylogenetic analysis reveals five independent transfers of the chloroplast gene rbcL to the mitochondrial genome in angiosperms. Current Genetics 43, 131–138.

Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32, 1792–1797.
MUSCLE: multiple sequence alignment with high accuracy and high throughput.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2cXisF2ks7w%3D&md5=3e700f813509cc233074b21dc7e451e8CAS |

Edwards EJ, Smith SA (2010) Phylogenetic analyses reveal the shady history of C4 grasses. Proceedings of the National Academy of Sciences of the United States of America 107, 2532–2537.
Phylogenetic analyses reveal the shady history of C4 grasses.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXit1aks7c%3D&md5=b0f2e298a02717f3ef683cb831195717CAS |

Eldridge DJ, Costantinides C, Vine A (2006) Short-term vegetation and soil responses to mechanical destruction of rabbit (Oryctolagus cuniculus L.) warrens in an Australian box woodland. Restoration Ecology 14, 50–59.
Short-term vegetation and soil responses to mechanical destruction of rabbit (Oryctolagus cuniculus L.) warrens in an Australian box woodland.Crossref | GoogleScholarGoogle Scholar |

Everett J, Jacobs SWL, Nairn L (2009) Austrostipa. In ‘Flora of Australia: 44A Poaceae 2’. (Ed. ABRS) pp. 15–62. (CSIRO: Melbourne)

Fazekas AJ, Burgess KS, Kesanakurti PR, Graham SW, Newmaster SG, Husband BC, Percy DM, Hajibabaei M, Barrett SCH (2008) Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well. PLoS ONE 3, e2802
Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well.Crossref | GoogleScholarGoogle Scholar |

Fehrer J, Gemeinholzer B, Chrtek J, Bräutigam S (2007) Incongruent plastid and nuclear DNA phylogenies reveal ancient intergeneric hybridization in Pilosella hawkweeds (Hieracium, Cichorieae, Asteraceae). Molecular Phylogenetics and Evolution 42, 347–361.
Incongruent plastid and nuclear DNA phylogenies reveal ancient intergeneric hybridization in Pilosella hawkweeds (Hieracium, Cichorieae, Asteraceae).Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28Xht1CgsbjO&md5=00231a7224c142ff575df0c0830464b4CAS |

Hsiao C, Jacobs SWL, Chatterton NJ, Asay KH (1999) A molecular phylogeny of the grass family (Poaceae) based on the sequences of nuclear ribosomal DNA (ITS). Australian Systematic Botany 11, 667–688.
A molecular phylogeny of the grass family (Poaceae) based on the sequences of nuclear ribosomal DNA (ITS).Crossref | GoogleScholarGoogle Scholar |

Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics (Oxford, England) 17, 754–755.
MRBAYES: Bayesian inference of phylogenetic trees.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BD3MvotV2isw%3D%3D&md5=36cced4192c095ad0b58c7c43beb4c9bCAS |

Huxtable CHA, Koen TB, Waterhouse D (2005) Establishment of native and exotic grasses on mine overburden and topsoil in the Hunter Valley, New South Wales. The Rangeland Journal 27, 73–88.
Establishment of native and exotic grasses on mine overburden and topsoil in the Hunter Valley, New South Wales.Crossref | GoogleScholarGoogle Scholar |

Jacobs SWL, Everett J (1996) Austrostipa, a new genus, and new names for Australian species formerly included in Stipa (Gramineae). Telopea 6, 579–595.

Jacobs SWL, Everett J, Barkworth ME, Hsiao C (2000) Relationships within the stipoid grasses (Gramineae). In ‘Grass systematics and evolution’. (Eds SWL Jacobs, J Everett) pp. 75–82. (CSIRO: Melbourne)

Jacobs SWL, Bayer R, Everett J, Arriaga MO, Barkworth ME, Sabin-Badereau A, Torres MA, Vazquez FM, Bagnall N (2007) Systematics of the tribe Stipeae (Gramineae) using molecular data. Aliso 23, 349–361.

Käss E, Wink M (1997) Molecular phylogeny and phylogeography of Lupinus (Leguminosae) inferred from nucleotide sequences of the rbcL gene and ITS 1 + 2 regions of rDNA. Plant Systematics and Evolution 208, 139–167.
Molecular phylogeny and phylogeography of Lupinus (Leguminosae) inferred from nucleotide sequences of the rbcL gene and ITS 1 + 2 regions of rDNA.Crossref | GoogleScholarGoogle Scholar |

Krause K (2008) From chloroplasts to ‘cryptic’ plastids: evolution of plastid genomes in parasitic plants. Current Genetics 54, 111–121.
From chloroplasts to ‘cryptic’ plastids: evolution of plastid genomes in parasitic plants.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXhtVWntr%2FK&md5=0b71620e89cc916fbadb78b19fefc4b5CAS |

Kress WJ, Erickson DL (2007) A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH–psbA spacer region. PLoS ONE 2, e508
A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH–psbA spacer region.Crossref | GoogleScholarGoogle Scholar |

Linder PH, Baeza M, Barker NP, Galley C, Humphreys A, Lloyd KM, Orlovich DA, Pirie MD, Simon BK, Walsh N, Verboom GA (2010) A generic classification of the Danthonioideae (Poaceae). Annals of the Missouri Botanical Garden 97, 306–364.
A generic classification of the Danthonioideae (Poaceae).Crossref | GoogleScholarGoogle Scholar |

Mallatt JM, Garey JR, Shultz JW (2003) Ecdysozoan phylogeny and Bayesian inference: first use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin. Molecular Phylogenetics and Evolution 31, 178–191.
Ecdysozoan phylogeny and Bayesian inference: first use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin.Crossref | GoogleScholarGoogle Scholar |

Marschner P, Solaiman Z, Rengel Z (2006) Rhizosphere properties of Poaceae genotypes under P-limiting conditions. Plant and Soil 283, 11–24.
Rhizosphere properties of Poaceae genotypes under P-limiting conditions.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XpvVGgsb0%3D&md5=c40c8bd121d16de9ee1a4b61bafc7f48CAS |

McLaren DA, Stajsic V, Iaconis L (2004) The distribution, impacts and identification of exotic stipoid grasses in Australia. Plant Protection Quarterly 19, 59–66.

Nie ZN, Zollinger RP, Jacobs JL (2009) Performance of 7 Australian native grasses from the temperate zone under a range of cutting and fertiliser regimes. Crop and Pasture Science 60, 943–953.
Performance of 7 Australian native grasses from the temperate zone under a range of cutting and fertiliser regimes.Crossref | GoogleScholarGoogle Scholar |

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

Pirie MD, Humphreys AM, Galley C, Barker NP, Verboom GA, Orlovich D, Draffin SJ, Lloyd K, Baeza CM, Negritto M, Ruiz E, Sanchez JHC, Reimer E, Linder HP (2008) A novel supermatrix approach improves resolution of phylogenetic relationships in a comprehensive sample of danthonioid grasses. Molecular Phylogenetics and Evolution 48, 1106–1119.
A novel supermatrix approach improves resolution of phylogenetic relationships in a comprehensive sample of danthonioid grasses.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXhtVynt7fN&md5=f4a1faff80cab15fe2e15bf794a98101CAS |

Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817–818.
MODELTEST: testing the model of DNA substitution.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK1MXktlCltw%3D%3D&md5=3d05fcb80b92fac912ffefaee08f7e4aCAS |

Prober SM, Thiele KR, Lunt ID (2002) Identifying ecological barriers to restoration in temperate grassy woodlands: soil changes associated with different degradation states. Australian Journal of Botany 50, 699–712.
Identifying ecological barriers to restoration in temperate grassy woodlands: soil changes associated with different degradation states.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3sXlvFamsw%3D%3D&md5=39f7bcd55c4eb2981d25ed18f699982dCAS |

Rambaut A (2009) ‘FigTree version 1.3.1.’ Available at http://tree.bio.ed.ac.uk/software/figtree [accessed September 2010].

Romaschenko K, Peterson PM, Soreng RJ, Garcia-Jacas N, Futorna O, Susanna A (2008) Molecular phylogenetic analysis of the American Stipeae (Poaceae) resolves Jarava sensu lato polyphyletic: evidence for a new genus, Pappostipa. Journal of the Botanical Research Institute of Texas 2, 165–192.

Romaschenko K, Peterson PM, Soreng RJ, Garcia-Jacas N, Futorna O, Susanna A (2010) Phylogenetics of Stipeae (Poaceae: Pooideae) based on plastid and nuclear DNA sequences. In ‘Diversity, phylogeny and evolution in the monocotyledons’. (Eds O Seberg, G Petersen, AS Barfod and JI Davis.) pp. 511–537. (Aarhus University Press: Denmark)

Schneider J, Doring E, Hilu KW, Roser M (2009) Phylogenetic structure of the grass subfamily Pooideae based on comparison of plastid matK gene3 trnK exon and nuclear ITS sequences. Taxon 58, 405–424.

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.
Phylogenetic analysis of Sorghum and related taxa using internal transcribed spacers of nuclear ribosomal DNA.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK2MXivFWkt7k%3D&md5=5c6de875b92adac672cbe1c47ee02554CAS |

Swofford DL (2003) ‘PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4.0b10.’ (Sinauer Associates: Sunderland, MA)

Taylor DJ, Piel WH (2004) An assessment of accuracy, error, and conflict with support values from genome-scale phylogenetic data. Molecular Biology and Evolution 21, 1812
An assessment of accuracy, error, and conflict with support values from genome-scale phylogenetic data.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2cXntVCitbk%3D&md5=9a7159bdd7c40a28920ed63e292bcc0dCAS |

Tsitrone A, Kirkpatrick M, Levin DA (2003) A model for chloroplast capture. Evolution 57, 1776–1782.

Turner SR, Merritt DJ, Renton MS, Dixon KW (2009) Seed moisture content affects afterripening and smoke responsiveness in three sympatric Australian native species from fire-prone environments. Austral Ecology 34, 866–877.
Seed moisture content affects afterripening and smoke responsiveness in three sympatric Australian native species from fire-prone environments.Crossref | GoogleScholarGoogle Scholar |

Vickery JW, Jacobs SWL, Everett J (1986) Taxonomic studies in Stipa (Poaceae) in Australia. Telopea 3, 1–132.

Walker J (2004) Claviceps phalaridis in Australia: biology, pathology and taxonomy with a description of the new genus Cepsiclava (Hypocreales, Clavicipitaceae). Australasian Plant Pathology 33, 211–239.
Claviceps phalaridis in Australia: biology, pathology and taxonomy with a description of the new genus Cepsiclava (Hypocreales, Clavicipitaceae).Crossref | GoogleScholarGoogle Scholar |

Wilgenbusch JC, Warren DL, Swofford D (2004) ‘AWTY: a system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference.’ Available at http://ceb.csit.fsu.edu/awty [accessed November 2012].

Wolfe AD, Randle CP (2004) Recombination, heteroplasmy, haplotype polymorphism, and paralogy in plastid genes: implications for plant molecular systematics. Systematic Botany 29, 1011–1020.
Recombination, heteroplasmy, haplotype polymorphism, and paralogy in plastid genes: implications for plant molecular systematics.Crossref | GoogleScholarGoogle Scholar |