A phylogenetic analysis of Dipsacaceae based on four DNA regions

Plant Systematics and Evolution

Volumn 279, Issue 1-4, 2009, Pages 69-86

  Avino, M ^a,b   Tortoriello, G ^a   Caputo, P ^a  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^b UNIVERSITY OF ALBERTA   (Canada)

Author keywords

Dipsacaceae; Internal transcribed spacers (ITS); Phylogeny; PsbB psbH; TrnL intron; TrnL trnF intergenic spacer

Indexed keywords

DIPSACACEAE; LOMELOSIA; PSEUDOSCABIOSA; PTEROCEPHALIDIUM; PTEROCEPHALUS; PYCNOCOMON; SUCCISA; SUCCISELLA;

EID: 67349232992     PISSN: 03782697     EISSN: 16156110     Source Type: Journal    
DOI: 10.1007/s00606-009-0147-y     Document Type: Article

References (77)

1. S Aceto P Caputo S Cozzolino L Gaudio A Moretti 1999 Phylogeny and evolution of Orchis and allied genera based on ITS DNA variation: morphological gaps and molecular continuity Mol Phylogenet Evol 13 67 76 (Pubitemid 129499320)
2. Backlund AA, Donoghue MJ (1996) Morphology and phylogeny of the order Dipsacales. In: Backlund AA (ed) Phylogeny of the Dipsacales, Doctoral Dissertation. Department of Systematic Botany, Uppsala University, Uppsala
3. BG Baldwin MJ Sanderson MJ Porter MF Wojciechowski CS Campbell MJ Donoghue 1995 The ITS region of nuclear ribosomal DNA: a valuable source of evidence in angiosperm phylogeny Ann Missouri Bot Gard 82 247 277
4. RJ Bayer DE Soltis PS Soltis 1996 Phylogenetic inferences in Antennaria (Asteraceae: Gnaphalieae: Cassiniinae) based on sequences from nuclear ribosomal DNA internal transcribed spacers (ITS) Am J Bot 83 516 527 (Pubitemid 126514369)
5. CD Bell 2004 Preliminary phylogeny of Valerianaceae (Dipsacales) inferred from nuclear and chloroplast DNA sequence data Mol Phylogenet Evol 31 340 350 (Pubitemid 38403341)
6. CD Bell MJ Donoghue 2003 Phylogeny of Morinaceae (Dipsacales) based on nuclear and chloroplast DNA sequences Org Div Evol 3 227 237 (Pubitemid 37171960)
7. CD Bell EJ Edwards ST Kim MJ Donoghue 2001 Dipsacales phylogeny based on chloroplast DNA sequences Harvard Pap Bot 6 481 499
8. K Bremer 1994 Branch support and tree stability Cladistics 10 295 304
9. AA Bukharov VL Kolosov AS Zolotarev 1988 Nucleotide sequence of rye chloroplast DNA fragment encoding psbB and psbH genes Nucl Acids Res 16 8737 (Pubitemid 18171875)
10. Burtt BL (1999) The importance of some far eastern species of Dipsacaceae in the history of the family. In: Tandon RK, Singh P (eds) Biodiversity, Taxonomy and Ecology: Prof. Dakshini K. M. M. Festschrift. Scientific Publishers, India, p 137
11. MJ Cannon JFM Cannon 1984 A revision of the Morinaceae (Magnoliophyta-Dipsacales). Bulletin of the British Museum (Natural History) Botany 12 1 35
12. P Caputo S Cozzolino 1994 A cladistic analysis of Dipsacaceae (Dipsacales) Plant Syst Evol 189 41 61 (Pubitemid 2034327)
13. P Caputo S Cozzolino A Moretti 2004 Molecular phylogenetics of Dipsacaceae reveals parallel trends in seed dispersal syndromes Plant Syst Evol 246 163 175 (Pubitemid 39059068)
14. CW Cunningham KE Omland TH Oakley 1998 Reconstructing ancestral character states: a critical reappraisal Tree 13 361 366 (Pubitemid 28385525)
15. De Laet J, Wheeler W (2003) POY version 3.0.11 (Wheeler, Gladstein, and De Laet, 6 May 2003). Command line documentation. Available from:
16. JA Devesa 1984 Pseudoscabiosa, genere nuevo de Dipsacaceae Lagascalia 12 213 221
17. MJ Donoghue T Eriksson PA Reeves RG Olmstead 2001 Phylogeny and phylogenetic taxonomy of Dipsacales, with special reference to Sinadoxa and Tetradoxa (Adoxaceae) Harvard Pap Bot 6 459 479 (Pubitemid 33017012)
18. MJ Donoghue CD Bell RC Winkworth 2003 The evolution of reproductive characters in Dipsacales J Plant Sci 164 5 Suppl S453 S464 (Pubitemid 37417958)
19. JJ Doyle JL Doyle 1990 Isolation of plant DNA from fresh tissue Focus 12 13 15
20. F Ehrendorfer 1962 Beiträge zur Phylogenie der Gattung Knautia (Dipsacaceae), I. Cytologische Grundlagen und allgemeine Hinweise Österr Bot Zeit 109 276 343
21. Ehrendorfer F (1964a) Cytologie, Taxonomie und Evolution bei Samenpflanzen. In: Turril WB (ed) Vistas in Botany. 4. The MacMillan Company, New York, pp 99-186
22. F Ehrendorfer 1964 Über stammesgeschichtliche Differenzierungsmuster bei den Dipsacaceen Ber Dtsch Bot Gesellsch 77 83 94
23. F Ehrendorfer 1965 Evolution and karyotype differentiation in a family of flowering plants: Dipsacaceae Genetics Today (Proc. XI International Congress of Genetics, The Hague, The Netherlands, 1963) 2 399 407
24. DP Faith PS Cranston 1991 Could a cladogram this short have arisen by chance alone? On permutation tests for cladistic structure Cladistics 7 1 28
25. BM Fangan B Stedje OE Stabbetorp ES Jensen KS Jakobsen 1994 A general approach for PCR amplification and sequencing of chloroplast DNA from crude vascular plant and algal tissue BioTechniques 16 484 494 (Pubitemid 2064257)
26. JS Farris M Källersjö AG Kluge C Bult 1994 Testing significance of incongruence Cladistics 10 315 319
27. J Felsenstein 1985 Confidence limits on phylogenies: an approach using the bootstrap Evolution 39 783 791
28. L Gielly P Taberlet 1995 Chloroplast DNA polymorphism at the intrageneric level: incidences in resolving plant phylogenies Compte Rendu de l'Academie des Sciences III, Sciences de la Vie 317 685 692
29. L Gielly P Taberlet 1995 The use of chloroplast DNA resolve plant phylogenesis: non-coding versus rbcL sequences Mol Biol Evol 11 769 777 (Pubitemid 24274885)
30. L Gielly P Taberlet 1996 A phylogeny of European gentians inferred from chloroplast trnL (UAA) intron sequences Bot J Linn Soc 120 57 75 (Pubitemid 26310482)
31. Goloboff P (1999a) Nona. Instruction manual. S. M. de Tucumán, Argentina
32. P Goloboff 1999 Analyzing large data sets in reasonable times: solutions for composite optima Cladistics 15 415 428 (Pubitemid 30203168)
33. Goloboff P, Farris JS, Nixon K (2003) TNT (tree analysis using new technology), Version 1.0. Published by the authors, Tucumán, Argentina
34. Greuter W, Burdet R (1985) Dipsacaceae. In: Greuter W, Raus T (eds) Med-Checklist Notulae 11. Willdenowia 15:71-76
35. S Guindon O Gascuel 2003 A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood Syst Biol 52 696 704 (Pubitemid 37365050)
36. M Hasegawa H Kishino T Yano 1985 Dating the human-ape splitting by a molecular clock of mitochondrial DNA J Mol Evol 22 160 174 (Pubitemid 16227864)
37. JP Huelsenbeck FR Ronquist 2001 MrBayes: Bayesian inference of phylogeny Biometrics 17 754 755
38. JP Huelsenbeck F Ronquist R Nielsen JP Bollback 2001 Bayesian inference of phylogeny and its impact on evolutionary biology Science 294 2310 2314 (Pubitemid 33140548)
39. WS Judd RW Sanders MJ Donoghue 1994 Angiosperm family pairs preliminary phylogenetic analyses Harvard Pap Bot 5 1 51 (Pubitemid 24181127)
40. C Lanave G Preparata C Saccone G Serio 1984 A new method for calculating evolutionary substitution rates J Mol Evol 20 86 93 (Pubitemid 14116237)
41. G López Gonzáles 1987 Pterocephalidium, un nuevo género ibérico de la familia Dipsacaceae Anales Jard Bot Madrid 43 245 252
42. Maddison WP, Maddison DR (2008) Mesquite: a modular system for evolutionary analysis. Version 2.5 http://mesquiteproject.org
43. B Mau M Newton 1997 Phylogenetic inference for binary data on dendrograms using Markov chain Monte Carlo J Comput Graph Stat 6 122 131 (Pubitemid 127175941)
44. B Mau M Newton B Larget 1999 Bayesian phylogenetic inference via Markov chain Monte Carlo methods Biometrics 55 1 12 (Pubitemid 29161999)
45. V Mayer F Ehrendorfer 1999 Fruit differentiation, palynology, and systematics in the Scabiosa group of genera and Pseudoscabiosa (Dipsacaceae) Plant Syst Evol 216 135 166 (Pubitemid 29184073)
46. V Mayer F Ehrendorfer 2000 Fruit differentiation, palynology, and systematics in Pterocephalus Adanson and Pterocephalodes, gen. nov. (Dipsacaceae) Bot J Linn Soc 132 47 78 (Pubitemid 30078991)
47. K Müller 2005 SeqState: primer design and sequence statistics for phylogenetic DNA datasets Appl Bioinformatics 4 65 69 (Pubitemid 41043903)
48. Nixon KC (1999) Winclada (beta) ver. 0.9.9. Published by the author, Ithaca
49. Nylander JAA (2004) MrAIC.pl. Program distributed by the author. Evolutionary Biology Centre, Uppsala University, Uppsala. http://www.abc.se/ ~nylander/
50. N Pyck E Smets 2004 On the systematic position of Triplostegia (Dipsacales): a combined molecular and morphological approach Belg J Bot 137 2 125 139 (Pubitemid 41132854)
51. B Rannala ZH Yang 1996 Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference J Mol Evol 43 304 311 (Pubitemid 26315133)
52. M Robinson M Gouy C Gautier D Mouchiroud 1998 Sensitivity of the relative-rate test to taxonomic sampling Mol Biol Evol 15 1091 1098 (Pubitemid 28394944)
53. M Robinson-Rechavi D Huchon 2000 RRTree: relative-rate tests between groups of sequences on a phylogenetic tree Bioinformatics 16 296 297 (Pubitemid 30352860)
54. Ronquist F, Huelsenbeck JP, van der Mark P (2005) MrBayes 3.1 manual, Draft 5/17/2005. http://mrbayes.csit.fsu.edu/mb3.1-manual.pdf (accessed 18 May 2005)
55. F Sanger S Niklen AR Coulson 1977 DNA sequencing with chain terminating inhibitors Proc Natl Acad Sci USA 74 5463 5467
56. HB Shaffer ML McKnight 1996 The polytypic species revisited: genetic differentiation and molecular phylogenetics of the tiger salamander Ambystoma tigrinum (Amphibia: Caudata) complex Evolution 50 417 433 (Pubitemid 3035503)
57. MP Simmons H Ochoterena 2000 Gaps as characters in sequence-based phylogenetic analyses Syst Biol 49 369 381
58. Y Suh LB Thien HE Reeve EA Zimmer 1993 Molecular evolution and phylogenetic implications of internal sequences of nuclear ribosomal DNA in Winteraceae Am J Bot 80 1042 1055
59. Y Sun DZ Skinner GH Liang SH Hulbert 1994 Phylogenetic analysis of Sorghum and related taxa using internal transcribed spacers of nuclear ribosomal DNA Theor Appl Genet 89 26 32 (Pubitemid 2155319)
60. P Taberlet L Gielly G Pautou J Bouvet 1991 Universal primers for amplification of three noncoding regions of chloroplast DNA Plant Mol Biol 17 1105 1109
61. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins 1997 The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucl Acids Res 24 4876 4882 (Pubitemid 28022245)
62. Van Steenis CGGJ (1948) Dipsacaceae. In: Van Steenis CGGJ (ed) Flora Malesiana 4. Noordhoff-Kolff N. V, Batavia, pp 290-292
63. R Verláque 1977 Rapports entre les Valerianaceae, les Morinaceae et les Dipsacaceae Bull Soc Bot Fr 124 475 482
64. R Verláque 1977 Importance du fruit dans la détermination des Dipsacaceae Bull Soc Bot Fr 124 515 527
65. Verláque R (1984a) A biosystematic and phylogenetic study of the Dipsacaceae. In: Grant R (ed) Plant biosystematics. Academic Press, Toronto, pp 307-320
66. R Verláque 1984 Etude biosystématique et phylogénétique des Dipsacaceae. I.-Délimitation des Dipsacaceae al' intérieur des Dipsacales, rapports avec les autres familles de l'ordre. Rev. Gén Bot 91 81 121
67. R Verláque 1985 Etude biosystématique et phylogénétique des Dipsacaceae. II-Caractères généraux des Dipsacaceae Rev Cytol Biol Végét Le Botaniste 8 117 168
68. R Verláque 1985 Etude biosystématique et phylogénétique des Dipsaceae. III-Tribus des Knautieae et des Dipsaceae Rev Cytol Biol Végét Le Botaniste 8 171 243
69. R Verláque 1986 Etude biosystématique et phylogénétique des Dipsacaceae. IV-Tribus des Scabioseae (phylum n-1, 2, 3) Rev Cytol Biol Végét Le Botaniste 9 5 72
70. R Verláque 1986 Etude biosystématique et phylogénétique des Dipsacaceae. V-Tribus des Scabioseae (phylum n- 4) et conclusion Rev Cytol Biol Végét Le Botaniste 9 97 176
71. F Weberling 1975 On the systematics of Nardostachys (Valerianaceae) Taxon 24 443 452
72. F Weberling 1978 Monographie der Gattung Nardostachys DC. (Valerianaceae) Bot Jahrb Syst 99 188 221
73. WC Wheeler 1996 Optimization alignment: the end of multiple sequence alignment in phylogenetics? Cladistics 12 1 9 (Pubitemid 126400313)
74. WC Wheeler 2003 Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search Cladistics 19 261 268 (Pubitemid 38069698)
75. WC Wheeler J Gatesy R DeSalle 1995 Elision: a method for accommodating multiple molecular sequence alignments with alignment-ambiguous sites Mol Phylogenet Evol 4 1 9
76. Wheeler WC, Gladstein DS, De Laet J, Aaronson L (2003) POY, ver. 3.0.11a. Available from http://research.amnh.org/scicomp/projects/poy.php
77. WH Zhang ZD Chen JH Li HB Chen YC Tang 2003 Phylogeny of the Dipsacales s.l. based on chloroplast trnL-F and ndhF sequences Mol Phylogenet Evol 26 176 189 (Pubitemid 36264250)