The higher-level phylogeny of monocots based on matK, rbcL and 18S rDNA sequences

Acta Phytotaxonomica Sinica

Volumn 45, Issue 2, 2007, Pages 113-133

  Li, Xiao Xian ^a   Zhou, Zhe Kun ^a  

^a KUNMING INSTITUTE OF BOTANY   (China)

Author keywords

18s rDNA; matK; Monocots; Petrosaviaceae; Phylogeny; rbcL

Indexed keywords

ACORACEAE; ACORALES; ACORUS; ALISMATALES; ARACEAE; ARECALES; ASPARAGALES; CANELLALES; COMMELINALES; DIOSCOREALES; LAURALES; LILIALES; LILIOPSIDA; MAGNOLIALES; MAGNOLIOPHYTA; NYMPHAEALES; PANDANALES; PETROSAVIACEAE; PIPERALES; POALES; TOFIELDIACEAE; ZINGIBERALES;

EID: 34247132504     PISSN: 05291526     EISSN: None     Source Type: Journal    
DOI: 10.1360/aps06148     Document Type: Article

References (46)

1. APG II. 2003. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Botanical Journal of the Linnean Society 141: 399-436.
2. Bharathan G, Zimmer E A. 1995. Early branching events in monocotyledons. In: Rudall P J, Crib P J, Cutler D F, Humphries C J eds. Monocotyledons: Systematics and Evolution. London: Royal Botanic Garden, Kew. 81-107.
3. Borsch T, Hilu K W, Quandt D, Wilde V, Neinhuis C, Barthlott W. 2003. Noncoding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms. Journal of Evolutionary Biology 16: 558-576.
4. Bull C, Kallersjo M, Suh Y. 1992. Amplification and sequencing of 16S/18S rDNA from gel purified total plant DNA. Plant Molecular Biology Reporter 10: 272-284.
5. Cai Z Q, Penaflor C, Kuehl J V, Leebens-Mack J, Varlson J E, dePamphilis C W, Boore J L, Jansen R K. 2006. Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids. BioMed Central Evolutionary Biology 6: 77.
6. Chase M W, Albert V A. 1998. A perspective on the contribution of plastid rbcL DNA sequences to angiosperm phylogenetics. In: Soltis D E, Soltis P S, Doyle J J eds. Molecular Systematics of Plants II: DNA Sequencing. Boston: Kluwer Academic Publishers. 488-507.
7. Chase M W, Cox A V. 1998. Gene sequences, collaboration, and analysis of large data sets. Australian Systematic Botany 11: 215-229.
8. Chase M W, Duval M R, Hills H G, Conran J G, Cox A V, Eguiarte L E, Hartwell J, Fay M F, Caddick L R, Cameron K M, Hoot S. 1995a. Molecular phylogenetics of Lilianae. In: Rudall P J, Crib P J, Cutler D F, Humphries C J eds. Monocotyledons: systematics and evolution. London: Royal Botanic Garden, Kew. 109-137.
9. Chase M W, Fay M F, Savolainen V. 2000. Higher-level classification in the angiosperms: new insights from the perspective of DNA sequence data. Taxon 49: 685-704.
10. Chase M W, Soltis D E, Olmstead R G Morgan D R, Les D H, Mishler B D, Duvall M R, Price R, Hills H G, Qiu Y L, Kron K A, Retting J H, Conti E, Palmer J D, Manhart J R, Sytsma K J, Michaels H J, Kress W J, Karol K G, Clark W D, Hedren M, Gaut B S, Jansen R K, Kim K J, Wimpee C F, Smith J F, Furnier G R, Strauss S H, Xiang Q Y, Plunkett G M, Soltis P S, Williams S E, Gadek P A, Quinn C J, Eguiarte, L. E., Golenberg E, Learn G H, Graham S, Barrett S C H, Dayanandan S, Albert V A. 1993. Phylogenetics of seed plants: An analysis of nucleotide sequences from the plastid gene rbcL. Annals of the Missouri Botanical Garden 80: 528-580.
11. Chase M W, Soltis D E, Soltis P S, Rudall P J, Fay M F, Hahn W H, Sullivan S, Joseph J, Molvray M, Kores P J, Givnish T J, Sytsma K J, Pipes J C. 2000. High-level systematics of the monocotyledons: an assessment of current knowledge and a new classification. In: Wilson K L, Morrison D A eds. Monocots: Systematics and Evolution. Collingwood: CSIRO. 3-16.
12. Chase M W, Stevenson D W, Wilkin P, Rudall P J. 1995b. Monocot systematics: a combined analysis. In: Rudall P J, Cribb P J, Cutler D F, Humphries C J eds. Monocots: Systematics and Evolution. London: Royal Botanic Garden, Kew. 685-730.
13. Chen Z-D, Lu A-M. 1997. Origin and early evolution of Angiosperms: retrospect and prospects. Acta Phytotaxonomica Sinica 34: 375-384.
14. Crane P R, Donoghue M J, Doyle J A, Friis EM. 1989. Angiosperm origins. Nature 342: 131.
15. Davis J I, Simmonds M P, Stevenson D W, Wendel J F. 1998. Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atpA sequences. Systematic Biology 47: 282-310.
16. Davis J I, Stevenson D W, Petersen G, Seberg O, Campbell L M, Freudenstein J V, Goldman D H, Hardy C R, Michelangeli F A, Simmons M P, Specht C D, Verga-Silva F, Gandolfo M. 2004. A phytogeny of the monocots, as inferred from rbcL and atpA sequence variation, and a comparison of methods for calculation jackknife and bootstrap values. Systematic Botany 29: 467-510.
17. Doyle J J, Doyle J L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11-15.
18. Doyle J A, Endress P K. 2000. Morphological phylogenetic analysis of basal angiosperms: comparison and combination with molecular data. International Journal of Plant Sciences 161 (6 Suppl.): S121-S153.
19. Duvall M W, Clegg M T, Chase M W, Clark W D, Kress W J, Hills H G, Eguiarte L E, Smith J F, Gaut B S, Zimmer E A, Learn G H. 1993. Phylogenetic hypotheses for the monocotyledons constructed from rbcL sequence data. Annals of the Missouri Botanical Garden 80: 607-619.
20. Feng Y-X, Wang X-Q, Pan K-Y, Hong D-Y. 1998. A revaluation of the systematic positions of the Cercidiphyllaceae and Daphniphyllaceae based on rbcL gene sequence analysis, with reference to the relationship in the "lower" Hamamelidae. Acta Phytotaxonomica Sinica 36:411-422.
21. Fuse S, Tamura M N. 2000. A phylogenetic analysis of the plastid matK. gene with emphasis on Melanthiaceae sensu lato. Plant Biology 2: 415-427.
22. Graham S M, Reeves P A, Burns ACE, Olmstead R G 2000. Microstructural changes in noncoding chloroplast DNA: interpretation, evolution, and utility of indels and inversions in basal angiosperm phylogenetic inference. International Journal of Plant Sciences 161 (6 Suppl.): S83-S96.
23. Graham S W, Olmstead R G. 2000. Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms. American Journal of Botany 87: 1712-1730.
24. Graham S W, Zgurski J M, Mcpherson M A, Cherniawsky D M, Saarela J M, Horne ESC, Smith S Y, Wong W A, O'Brien H E, Biron V L, Pires C P, Olmstead R G, Chase M W, Rai H S. 2006. Robust inference of monocot deep phylogeny using an expanded multigene plastid data set. In: Columbus J T, Friar E A, Hamilton C W, Porter J M, Prince L M, Simpson M G eds. Monocots: Comparative Biology and Evolution, Rancho Santa Ana Botanical Garden, Claremont, CA (in press).
25. Hillis D M, Dixon M T. 1991. Ribosomal DNA: molecular evolution and phylogenetic inference. The Quarterly Review of Biology 66: 411-453.
26. Hilu K W, Borsch T, Muller K, Soltis D E, Soltis P S, Savolainen V, Chase M W, Powell M P, Alice L A, Evans R, Sauquet H, Neinhuis C, Slotta TAB, Rohwer J G, Campbell C S, Chatrou L W. 2003.
27. Angiosperm phylogeny based on matK sequence information. American Journal of Botany 90: 1758-1776.
28. Johnson L A, Soltis D E. 1994. matK. DNA sequences and phylogenetic reconstruction in the Saxifragaceae sensu stricto. Systematic Botany 19: 143-156.
29. Les D H, Cleland M A, Waycott M. 1997. Phylogenetic studies in Alismatidae, II: evolution of marine angiosperms (seagrasses) and hydrophily. Systematic Botany 22: 443-463.
30. Mathews S, Donoghue M J. 1999. The root of angiosperm phylogeny inferred from duplicate phytochrome genes. Science 286: 947-950.
31. Nadot S, Bittar G, Carter L, Lacroix R, Lejeune B. 1995. A phylogenetic analysis of monocotyledons based on the chloroplast gene rps4, using parsimony and a new numerical phenetics method. Molecular Phylogenetics and Evolution 4: 257-282.
32. Nandi O I, Chase M W, Endress P K. 1998. A combined cladistic analysis of angiosperms using rbcL and non-molecular data sets. Annals of the Missouri Botanical Garden 85: 137-212.
33. Nickrent D L, Blarer A, Qiu Y L, Soltis D E, Soltis P S, Zanis M. 2002. Molecular data place Hydnoraceae with Aristolochiaceae. American Journal of Botany 89: 1809-1817.
34. Qiu Y L, Dombrovska O, Lee J, Li L, Whitlock B A, Bernasconi-Quadroni F, Rest J S, Davis C C, Borsch T, Hilu K W, Renner S S, Soltis D E, Soltis P S, Zanis M J, Cannone J J, Gutell R R, Powell M, Savolainen V, Chatrou L W, Chase M W. 2005. Phylogenetic analysis of basal angiosperms based on nine plastid, mitochondrial, and nuclear genes. International Journal of Plant Sciences 166: 815-842.
35. Qiu Y L, Lee J, Bernasconi-Quadroni F, Soltis D E, Soltis P S, Zanis M, Zimmer E A, Chen Z, Savolainen V, Chase M W. 1999. The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes. Nature 402: 404-407.
36. Qiu Y L, Lee J, Bernasconi-Quadroni F, Soltis D E, Soltis P E, Zanis M, Zimmer E A, Chen Z, Savolainen V, Chase M W. 2000. Phylogeny of basal angiosperms: analyses of five genes from three genomes. International Journal of Plant Sciences 161 (Suppl.): 3-27.
37. Qiu Y L, Li L, Hendry T A, Li R, Taylor D W, Issa M J, Ronen A J, Vekaria M L, White A M. 2006. Reconstructing the basal angiosperm phylogeny: evaluating information content of the mitochondrial genes. Taxon 55: 837-856.
38. Qiu Y L, Palmer J D. 2004. Many independent origins of trans-splicing of a plant mitochondrial group II intron. Journal of Molecular Evolution 59: 80-89. Savolainen V, Chase M W, Hoot S B, Morton C M, Soltis D E, Bayer C, Fay M F, De Bruijn A Y, Sullivan S, Qiu Y L. 2000a. Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences. Systematic Biology 49: 306-362.
39. Savolainen V, Fay M F, Albach D C, Backlund A, van der Bank M, Cameron K. M, Johnson S A, Lledó M D, Pintaud J C, Powell M, Sheahan M C, Soltis D E, Soltis P S, Weston P, Whitten W M, Wurdack K J,
40. Chase M W. 2000b. Phylogeny of the eudicots: a nearly complete familial analysis based on rbcL gene sequences. Kew Bulletin 55: 257-309.
41. Soltis D E, Soltis P S, Nickrent D L, Johnson L A, Hahn W J, Hoot S B, Sweere J A, Kuzoff R K, Kron K A, Chase M W, Swensen S M, Zimmer E A, Chaw S M, Gillespie L J, Kress W J, Sytsma K J. 1997. Angiosperm phylogeny inferred from 18S ribosomal DNA sequences. Annals of the Missouri Botanical Garden 84: 1-49.
42. Soltis D E, Soltis P S, Chase M W, Mort M E, Albach D C, Zanis M, Savolainen V, Hahn W H, Hoot S B, Fay M F, Axtell M, Swensen S M, Prince L M, Kress W J, Nixon K C, Farris J S. 2000. Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences. Botanical Journal of the Linnean Society 133:381-461.
43. Stevenson D W, Davis J I, Freudenstein J V, Hardy C R, Simmons M P, Specht C D. 2000. A phylogenetic analysis of monocotyledons based on morphological and molecular character sets, with comments on the placement of Acorus and Hydatellaceae. In: Wilson K L, Morrison D A eds. Monocots: Systematics and Evolution. Collingwood: CSIRO. 17-24.
44. Swofford D L. 2001. PAUP*: phylogenetic analysis using parsimony, version 4.0b8. Sunderland, Massachusetts: Sinauer Associates.
45. Wu Z-Y, Lu A-M, Tang Y-C, Chen Z-D, Li D-Z. 2003. The Families and Genera of Angiosperms in China - A Comprehensive Analysis. Beijing: Science Press. Zanis M J, Soltis D E, Soltis P S, Mathews S, Donoghue M J. 2002. The root of the angiosperms revisited. Proceedings of the National Academy of Sciences 99: 6848-6853.
46. Zanis M J, Soltis D E, Soltis P S, Qiu Y L, Zimmer E A. 2003. Phylogenetic analyses and perianth evolution in basal angiosperms. Annals of the Missouri Botanical Garden 90: 129-150.