Phylogenetics of Panicoideae (Poaceae) based on chloroplast and nuclear DNA sequences

Telopea

Volumn 13, Issue 1-2, 2010, Pages 115-142

  Teerawatananon, Atchara ^a,b   Jacobs, Surrey W L ^c   Hodkinson, Trevor R ^b  

^a Ministry of Higher Education Science Research and Innovation   (Thailand)

^b TRINITY COLLEGE DUBLIN   (Ireland)

^c ROYAL BOTANIC GARDENS AND DOMAIN TRUST   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ANDROPOGONEAE; ARISTIDOIDEAE; ARUNDINELLA; ARUNDINELLEAE; ARUNDINOIDEAE; CENCHRUS; CHLORIDOIDEAE; DANTHONIOIDEAE; DANTHONIOPSIS; ERIACHNE; ERIACHNEAE; GARNOTIA; HOMOPHOLIS; ISACHNE; ISACHNEAE; MICRAIREAE; MICRAIROIDEAE; PANICEAE; PANICOIDEAE; POACEAE; TRISTACHYA;

EID: 79957521169     PISSN: 03129764     EISSN: None     Source Type: Journal    
DOI: 10.7751/telopea20116009     Document Type: Article

References (66)

1. Aliscioni SS, Giussani LM, Zuloaga FO & Kellogg EA (2003) A molecular phylogeny of Panicum (Poaceae: Paniceae): tests of monophyly and phylogenetic placement within the Panicoideae. American Journal of Botany 90: 796-821. (Pubitemid 36599675)
2. Baldwin BG, Sanderson M J, Porter JM, Wojciechowski MF, Campbell C&Donoghue MJ (1995) The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Annals of the Missouri Botanical Gardens 82: 247-277.
3. Barker NP, Linder HP&Harley EH (1999) Sequences of the grass-specific insert in the chloroplast rpoC2 gene elucidate generic relationships of the Arundinoideae (Poaceae). Systematic Botany 23: 327-350. (Pubitemid 29285162)
4. Bentham G (1882) Notes on Gramineae. The Journal of the Linnean Society 19: 14-134.
5. Bess EC, Doust AN&Kellogg EA (2005) A naked grass in the "bristle clade": a phylogenetic and developmental study of Panicum section Bulbosa (Paniceae: Poaceae). International Journal of Plant Sciences 166: 371-381. (Pubitemid 40600456)
6. Bomblies K&Doebley J (2005) Pleiotropic effects of the duplicate maize FLORICAULA/LEAFY genes zfll and zfl2 on traits under selection during maize domestication. Genetics 172: 519531.
7. Bor NL (1955) Notes on Asiatic grasses XXIII: Jansenella Bor, a new genus of Indian grasses. Kew Bulletin 1955: 93-99.
8. 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.
9. Chase MW&Hills HH (1991) Silica gel: an ideal material for field preservation of leaf samples for DNA studies. Taxon 40: 215-220.
10. 4 photosynthesis in grasses. Current Biology 18: 37-43.
11. Clayton WD (1972) The awned genera of Andropogoneae: studies in the Gramineae XXXI. Kew Bulletin 27: 457-474.
12. Clayton WD (1973) Studies in the Gramineae XXXIII: the awnless genera of Andropogoneae. Kew Bulletin 28: 49-58.
13. Clayton WD&Renvoize SA (1986) Genera Graminum. Grasses of the world. Kew Bulletin, Additional Series 13: 1-389.
14. Davidse G&Ellis RP (1984) Steyermarkochloa unifolia, a new genus from Venezuela and Columbia (Poaceae: Arundinoideae: Steyermarkochloeae). Annals of the Missouri Botanical Garden 71: 994-1012.
15. Davidse G&Ellis RP (1987) Arundoclaytonia, a new genus of Steyermarkochloeae (Poaceae: Arundinoideae) from Brazil. Annals of the Missouri Botanical Garden 74: 479-490.
16. De Wet JMJ & Harlan JR (1966) Morphology of the compilospecies Bothriochloa intermedia. American Journal of Botany 53: 94-98.
17. De Wet JMJ&Harlan JR (1970) Bothriochloa intermedia. A taxonomic dilemma. Taxon 19: 339-340.
18. Donadio S, Giussani LM, Kellogg EA, Zuolaga FO & Morrone O (2009) A preliminary molecular phylogeny of Pennisetum and Cenchrus (Poaceae-Paniceae) based on the trnL-F, rpl 16 chloroplast markers. Taxon 58: 392-404.
19. Doust AN&Kellogg EA (2002) Inflorescence diversification in the panicoid "bristle grass" clade (Paniceae, Poaceae): evidence from molecular phylogenies and developmental morphology. American Journal of Botany 89: 1203-1222.
20. Doust AN, Penly AM, Jacobs SWL&Kellogg EA (2007) Congruence, conflict, and polyploidization shown by nuclear and chloroplast markers in the monophyletic "bristle clade" (Paniceae, Panicoideae, Poaceae). Systematic Botany 32: 531-544. (Pubitemid 350057073)
21. Doyle JJ & Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin for the Botany Society of America 19: 11-15.
22. Duvall MR, Davis JI, Clark LG, Noll JD, Goldman DH & Sánchez-Ken JG (2007) Phylogeny of the grasses (Poaceae) revisited. Aliso 23: 237-247.
23. Felsenstein J (1985) Confidence limits on phytogenies: an approach using the bootstrap. Evolution 39: 783-791.
24. Giussani LM, Cota-Sanches JH, Zuloaga FO Kellogg EA (2001) A molecular phylogeny of the grass subfamily Panicoideae (Poaceae) shows multiple origins of C4 photosynthesis. American Journal of Botany 88: 1993-2012. (Pubitemid 33649780)
25. Gomez-Martinez R & Culham A (2000) Phylogeny of the subfamily Panicoideae with emphasis on the tribe Paniceae: evidence from the trnL-F chloroplast DNA region. Pp. 136-140 in Jacobs SWL&Everett J (eds) Grasses: Systematics and Evolution. (Collingwood, Victoria: CSIRO Publishing)
26. GPWG (2001) Phylogeny and subfamily classification of the grasses (Poaceae). Annals of the Missouri Botanical Garden 88: 373-430.
27. Hackel E (1889) Andropogoneae. Pp. 1-716 in De Candolle A&De Candolle C (eds) Monographiae Phanerogamarum, vol. 6.(Sumptibus G. Masson: Paris)
28. Harlan JR & De Wet JMJ (1963) The compilospecies concept. Evolution 17: 497-501.
29. Hillis DM, Pollock DD, McGuire JA&Zwickl DJ (2003) Is sparse taxon sampling a problem for phylogenetic inference? Systematic Biology 52: 124-126. (Pubitemid 36300065)
30. Hilu KW&Wright K (1982) Systematics of Gramineae: a cluster analysis study. Taxon 31: 9-36.
31. Hilu KW, Alice LA & Liang HP (1999) Phylogeny of Poaceae inferred from matK sequences. Annals of the Missouri Botanical Garden 86: 835-851. (Pubitemid 30065557)
32. Hodkinson TR, Salamin N, Chase MW, Bouchenak-Khelladi Y, Renvoize SA & Savolainen V (2007a) Large trees, supertrees and diversification of the grass family. Aliso 23: 248-258.
33. Hodkinson TR, Waldren S, Parnell JAN, Kelleher CT, Salamin K&Salamin N (2007b) DNA banking for plant breeding, biotechnology and biodiversity evaluation. Journal of Plant Research 120: 17-29.
34. Huelsenbeck JP & Ronquist F (2001) MrBayes: Bayesian inference of phylogeny. Bioinformatics 17: 754-755.
35. 3 photosynthesis. Annals of Botany 103: 127-136.
36. Jannink TA&Veldkamp JF (2002) Revision of Chionachninae (Gramineae: Andropogoneae). Blumea 47: 545-580.
37. Kelchner SA (2000) The evolution of non-coding chloroplast DNA and its application in plant systematics. Annals of the Missouri Botanical Garden 87: 182-198.
38. Kellogg EA (2000) Molecular and morphological evolution in Andropogoneae. Pp. 149-158 in Jacobs SWL & Everett J (eds) Grasses: Systematics and Evolution. (CSIRO Publishing: Collingwood)
39. Kellogg EA & Campbell CS (1987) Phylogenetic nalyses of the Gramineae. Pp. 310-322 in Soderstrom TR, Hilu KW, Campbell CS&Barkworth ME (eds) Grass Systematics and Evolution. (Smithsonian Press: Washington, D.C)
40. Kellogg EA & Watson L (1993) Phylogenetic studies of a large dataset. I. Bambusoideae, Andropogonodae and Pooideae (Gramineae). Botanical Review 59: 273-343.
41. Mathews S, Spangler RE, Mason-Gamer RJ & Kellogg EA (2002) Phylogeny of Andropogoneae inferred from phytochrome B, GBSSI and ndhF. International Journal of Plant Sciences 163: 441-150.
42. Moore MJ, Bell CD,Soltis PS & Soltis DE (2007) Using plastid genomic-scale data to resolve enigmatic relationships among basal angiosperms. Proceedings of the National Academy of Sciences 104: 19363-19368.
43. Phipps JB (1966) Studies in the Arundinelleae III: check-list and key to the genera. Kirkia 5: 235-258.
44. Pirie MD, Humphreys AM, Galley C, Barker NP, Verboom GA, Orlovich D, Draffin SJ, Lloyd K, Baeza CM, Negritto M, Ruiz E, Cota-Sánchez JH, 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.
45. Posada D & Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 49: 817-818.
46. Rambaut A (1996) Se-Al Sequence Alignment Editor, vers. 2.0a11. (University of Oxford: Oxford)
47. , Rudall P, Fay MF, Cox AV, Lejeune B & Souza-Chies T (2001) Molecular systematics of Iridaceae: evidence from four plastid DNA regions. American Journal of Botany 88: 2074-2087.
48. Renvoize SA & Clayton WD (1992) Classification and evolution of grasses. Pp. 3-37 in Chapman GP (ed.) Grass Evolution and Domestication. (Cambridge University Press: Cambridge)
49. Samuel R, Pinsker W & Kiehn M (1997) Phylogeny of some species of Cyrtandra (Gesneriaceae) inferred from the atpß/rbcL cpDNA intergene region. Botánica Acta 110: 503-510. (Pubitemid 28014083)
50. Sánchez-Ken JG & Clark LG (2001) Gynerieae: a new neotropical tribe of grasses (Poaceae). Novon 11 : 350-352.
51. Sánchez-Ken JG, Clark LG, Kellogg EA & Kay EE (2007) Reinstatement and emendation of subfamily Micrairoideae (Poaceae). Systematic Botany 32: 71-80. (Pubitemid 46572372)
52. Sánchez-Ken JG & Clark LG (2007) Phylogenetic relationships within the Centothecoideae + Panicoideae clade (Poaceae) based on ndhF and rpl 16 sequences and structural data. Aliso 23 : 487-502.
53. Skendzic EM, Columbus JT & Cerros-Tlatilpa R (2007) Phylogenetics of Andropogoneae (Poaceae: Panicoideae) based on nuclear ribosomal internal transcribed spacer and chloroplast trnL-F sequences. Aliso 23 : 530-544.
54. Spangler R, Zaitchick B, Russo E & Kellogg EA (1999) Andropogoneae evolution and generic limits in Sorghum (Poaceae) using ndhF sequences. Systematic Botany 24 : 267-283.
55. Steudel EG (1854) Synopsis plantarum glumacearum, vol. 1. (J. B. Metzler: Stuttgart)
56. 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. (Pubitemid 2155319)
57. Swofford DL (2002) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods) vers. 4.0b10. (Sinauer Associates: Sunderland)
58. Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17 : 1105-1109.
59. Tateoka T (1958) Note on some grasses VIII: on leaf structure of Arundinella and Garnotia. Botanical Gazette 20: 101-109.
60. Tateoka T (1962) Starch grains of endosperm in grass systematics. Botanical Magazine, Tokyo 75: 377-383.
61. Teerawatananon A & Hodkinson TR (2008) Jansenella griffthiana (Müll. Hal.) Bor (Gramineae/Poaceae): a new record for Thailand. Thai Forest Bulletin (Botany) 36: 109-113.
62. Thomson JA (2002) An improved non-crogenic transport and storage preservative facilitating DNA extraction from 'difficult' plants collected at remote sites. Telopea 9: 755-760.
63. 4 photosynthesis. Global Change Biology 14: 2693-2977.
64. Watson L & Dallwitz MJ (1992 onwards) The grass genera of the world: descriptions, illustrations, identification, and information retrieval; including synonyms, morphology, anatomy, physiology, phytochemistry, cytology, classification, pathogens, world and local distribution, and references. (http://delta-intkey.com) (Downloaded 02 March 2009).
65. Wills KE, Whalley RDB & Brühl JJ (2000) Systematic studies in Paniceae (Poaceae): Homopholis and Whalleya gen. et sp nov. Australian Systematic Botany 13: 437-468. (Pubitemid 30466961)
66. Wortley AH, Rudall PJ, Harris DJ & Scotland RW (2005) How much data are needed to resolve a difficult phylogeny?: case study in Lamiales. Systematic Biology 54: 697-709.