Tree ferns: Monophyletic groups and their relationships as revealed by four protein-coding plastid loci

Molecular Phylogenetics and Evolution

Volumn 39, Issue 3, 2006, Pages 830-845

  Korall, Petra ^a,b   Pryer, Kathleen M ^a   Metzgar, Jordan S ^a   Schneider, Harald ^c   Conant, David S ^d  

^a DUKE UNIVERSITY   (United States)

^b SWEDISH MUSEUM OF NATURAL HISTORY   (Sweden)

^c UNIVERSITY OF GÖTTINGEN   (Germany)

^d LYNDON STATE COLLEGE   (United States)

Author keywords

atpA; atpB; Cyatheaceae; Dicksoniaceae; Hymenophyllopsidaceae; Long branch attraction; Lophosoriaceae; Loxomataceae; Metaxyaceae; Phylogeny; Plagiogyriaceae; rbcL; rps4; Tree ferns

Indexed keywords

PRIMER DNA; VEGETABLE PROTEIN;

ARTICLE; CLASSIFICATION; FERN; GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLASTID; STATISTICAL MODEL;

BASE SEQUENCE; DNA PRIMERS; FERNS; LIKELIHOOD FUNCTIONS; PHYLOGENY; PLANT PROTEINS; PLASTIDS;

CALOCHLAENA; CIBOTIUM; CULCITA (FERN); CYATHEACEAE; DICKSONIA; DICKSONIACEAE; FILICOPHYTA; HYMENOPHYLLOPSIDACEAE; LOPHOSORIACEAE; LOXOMATACEAE; METAXYACEAE; PLAGIOGYRIACEAE; THYRSOPTERIS;

EID: 33646436974     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2006.01.001     Document Type: Article

References (75)

1. Alfaro M.E., Zoller S., and Lutzoni F. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol. Biol. Evol. 20 (2003) 255-266
2. Anderson F.E., and Swofford D.L. Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA. Mol. Phylogenet. Evol. 33 (2004) 440-451
3. Bergsten J. A review of long-branch attraction. Cladistics 21 (2005) 163-193
4. Ching R.C. The fern genus Plagiogyria on the mainland of Asia. Acta Phytotax. Sin. 7 (1958) 105-154
5. Christensen C. Filicinae. In: Verdoorn F. (Ed). Manual of Pteridology (1938), Martinus Nijhoff, The Hague 522-550
6. Conant D.S. A revision of the genus Alsophila (Cyatheaceae) in the Americas. J. Arnold Arboretum 64 (1983) 333-382
7. Conant D.S., Raubeson L.A., Attwood D.K., Perera S., Zimmer E.A., Sweere J.A., and Stein D.B. Phylogenetic and evolutionary implications of combined analysis of DNA and morphology in the Cyatheaceae. In: Camus J.M., Gibby M., and Johns R.J. (Eds). Pteridology in Perspective (1996), Royal Botanic Gardens, Kew 231-248
8. Conant D.S., Raubeson L.A., Attwood D.K., and Stein D.B. The relationships of Papuasian Cyatheaceae to New World tree ferns. Am. Fern J. 85 (1995) 328-340
9. Conant D.S., Stein D.B., Valinski A.E.C., and Sudarsanam P. Phylogenetic implications of chloroplast DNA variation in the Cyatheaceae. I. Syst. Bot. 19 (1994) 60-72
10. Croft J.R. The stipe and rachis vasculature of the dicksonioid fern, Cystodium sorbifolium (Cystodiaceae). Kew Bull. 41 (1986) 789-803
11. Des Marais D.L., Smith A.R., Britton D.M., and Pryer K.M. Phylogenetic relationships and evoution of extant horsetails, Equisetum, based on chloroplast DNA sequence data (rbcL and trnL-F). Int. J. Plant Sci. 164 (2003) 737-751
12. Douady C.J., Delsuc F., Boucher Y., Doolittle W.F., and Douzery E.J.P. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol. Biol. Evol. 20 (2003) 248-254
13. Dubuisson J.-Y., Hennequin S., Douzery E.J.P., Cranfill R.B., Smith A.R., and Pryer K.M. rbcL phylogeny of the fern genus Trichomanes (Hymenophyllaceae), with special reference to neotropical taxa. Int. J. Plant Sci. 164 (2003) 753-761
14. Erixon P., Svennblad B., Britton T., and Oxelman B. Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Syst. Biol. 52 (2003) 665-673
15. Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27 (1978) 401-410
16. Felsenstein J. Inferring Phylogenies (2004), Sinauer Associates, Sunderland, Massachusetts
17. Gastony G.J. Spore morhology in the Dicksoniaceae. I. The genera Cystodium, Thyrsopteris, and Culcita. Am. J. Bot. 68 (1981) 808-819
18. Gastony G.J., and Tryon R.M. Spore morphology in Cyatheaceae. 2. Genera Lophosoria, Metaxya, Sphaeropteris, Alsophila, and Nephelea. Am. J. Bot. 63 (1976) 738-758
19. Geiger J.M.O., and Ranker T.A. Molecular phylogenetics and historical biogeography of Hawaiian Dryopteris (Dryopteridaceae). Mol. Phylogenet. Evol. 34 (2005) 392-407
20. Guindon S., and Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52 (2003) 696-704
21. Hasebe M., Omori T., Nakazawa M., Sano T., and Kato M. rbcL gene sequences provide evidence for the evolutionary lineages of leptosporangiate ferns. Proc. Natl. Acad. Sci. USA 91 (1994) 5730-5734
22. Hasebe M., Wolf P.G., Pryer K.M., Ueda K., Ito M., Sano R., Gastony G.J., Yokoyama J., Manhart J.R., Murakami N., Crane E.H., Haufler C.H., and Hauk W.D. Fern phylogeny based on rbcL nucleotide sequences. Am. Fern J. 85 (1995) 134-181
23. Hauk W.D., Parks C.R., and Chase M.W. Phylogenetic studies of Ophioglossaceae: evidence from rbcL and trnL-F plastid DNA sequences and morphology. Mol. Phylogenet. Evol. 28 (2003) 131-151
24. Hennequin S., Ebihara A., Ito M., Iwatsuki K., and Dubuisson J.-Y. Molecular systematics of the fern genus Hymenophyllum s. l. (Hymenophyllaceae) based on chloroplastic coding and noncoding regions. Mol. Phylogenet. Evol. 27 (2003) 283-301
25. Holttum R.E. The scales of Cyatheaceae (with special reference to the genus Schizocaena J. Sm.). Kew Bull. 12 (1957) 41-45
26. Holttum R.E. Cyatheaceae. In: Van Steenis C.G.G.J., and Holttum R.E. (Eds). Flora Malesiana. Martinus Nijhoff (1963), Dr. W. Junk Publishers, The Hague, Boston, London
27. Holttum R.E. The tree-ferns of Africa. Kew Bull. 36 (1981) 463-482
28. Holttum R.E., and Edwards P. The tree ferns of Mt. Roraima and neighbouring areas of the Guayana Highlands with comments on the family Cyatheaceae. Kew Bull. 38 (1983) 155-188
29. Holttum R.E., and Sen U. Morphology and classification of the tree ferns. Phytomorphol. 11 (1961) 406-420
30. Korall, P., Conant, D.S., Schneider, H., Ueda, K., Nishida, H., Pryer, K.M. In press. Phylogenetic position of Cystodium: It's not a tree fern - it's a polypod! Amer. Fern J.
31. Kubitzki K. The Families and Genera of Vascular Plants. In: Kramer K.U., and Green P.S. (Eds). Pteridophytes and Gymnosperms vol. 1 (1990), Springer-Verlag, Berlin, Germany
32. Lantz T.C., Rothwell G.W., and Stockey R.A. Conantiopteris schuchmanii, gen. et spec. nov., and the role of fossils in resolving the phylogeny of Cyatheaceae s.l. J. Plant Res. 112 (1999) 361-381
33. Large M.F., and Braggins J.E. Tree Ferns (2004), Timber Press, Portland/Cambridge
34. Lellinger D.B. Hymenophyllopsidaceae. Mem. N.Y. Bot. Gard. 38 (1984) 2-9
35. Lellinger D.B. The disposition of Trichopteris (Cyatheaceae). Am. Fern J. 77 (1987) 90-94
36. Lellinger D.B. Hymenophyllopsidaceae. In: Berry P.E., Holst B.K., and Yatskievych K. (Eds). Flora of the Venezuelan Guayana: Pteridophytes, Spermatophytes Acanthaceae-Araceae (1995), Missouri Botanical Garden and Timber Press, St. Louis and Portland
37. Lewis P.O., Holder M.T., and Holsinger K.E. Polytomies and Bayesian phylogenetic inference. Syst. Biol. 54 (2005) 241-253
38. Lucansky T.W. Comparative studies of the nodal and vascular anatomy in the neotropical Cyatheaceae. I. Metaxya and Lophosoria. Am. J. Bot. 61 (1974) 464-471
39. Lucansky T.W. Anatomical studies of the neotropical Cyatheaceae. II. Metaxya and Lophosoria. Am. Fern J. 72 (1982) 19-28
40. Maddison, D.R., Maddison, W.P., 2005. MacClade version 4.07. Sinauer Associates, Sunderland, Massachusetts, USA.
41. Nadot S., Bajon R., and Lejeune B. The chloroplast gene rps4 as a tool for the study of Poaceae phylogeny. Plant Syst. Evol. 191 (1994) 27-38
42. Nylander, J.A.A., 2004. MrAIC.pl version 1.4. Program distributed by the author. Evolutionary Biology Centre, Uppsala University. .
43. Pichi Sermolli R.E.G. Tentamen Pteridophytorum. Webbia 31 (1977) 315-512
44. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
45. Pryer K.M., Schneider H., Smith A.R., Cranfill R., Wolf P.G., Hunt J.S., and Sipes S.D. Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants. Nature 409 (2001) 618-622
46. Pryer K.M., Schuettpelz E., Wolf P.G., Schneider H., Smith A.R., and Cranfill R. Phylogeny and evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences. Am. J. Bot. 91 (2004) 1582-1598
47. Pryer K.M., Smith A.R., Hunt J.S., and Dubuisson J.-Y. rbcL data reveal two monophyletic groups of filmy ferns (Filicopsida: Hymenophyllaceae). Am. J. Bot. 88 (2001) 1118-1130
48. Pryer K.M., Smith A.R., and Skog J.E. Phylogenetic relationships of extant ferns based on evidence from morphology and rbcL sequences. Am. Fern J. 85 (1995) 205-282
49. Qiu Y.-J., White R.A., and Turner M.D. The developmental anatomy of Metaxya rostrata (Filicales: Metaxyaceae). Am. J. Bot. 82 (1995) 969-981
50. Rambaut, A., Drummond, A, 2005. Tracer version 1.2.1. Computer program distributed by the authors. Department of Zoology, University of Oxford. UK. .
51. Ranker T.A., Smith A.R., Parris B.S., Geiger J.M.O., Haufler C.H., Straub S.C.K., and Schneider H. Phylogeny and evolution of grammitid ferns (Grammitidaceae): a case of rampant morphological homoplasy. Taxon 53 (2004) 415-428
52. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
53. Rothwell G.W. Fossils and ferns in the resolution of land plant phylogeny. Bot. Rev. 65 (1999) 188-218
54. Rouhan G., Dubuisson J.Y., Rakotondrainibe F., Motley T.J., Mickel J.T., Labat J.N., and Moran R.C. Molecular phylogeny of the fern genus Elaphoglossum (Elaphoglossaceae) based on chloroplast non-coding DNA sequences: contributions of species from the Indian Ocean area. Mol. Phylogenet. Evol. 33 (2004) 745-763
55. Schneider H. The root anatomy of ferns: a comparative study. In: Camus J.M., Gibby M., and Johns R.J. (Eds). Pteridology in Perspective (1996), Royal Botanic Gardens, Kew 271-283
56. Schneider H., Janssen T., Hovenkamp P., Smith A.R., Cranfill R., Haufler C.H., and Ranker T.A. Phylogenetic relationships of the enigmatic malesian fern Thylacopteris (Polypodiaceae, Polypodiidae). Int. J. Plant Sci. 165 (2004) 1077-1087
57. Schneider H., Ranker T.A., Russell S.J., Cranfill R., Geiger J., Aguraijua R., Wood K.R., Grundmann M., and Vogel J.C. Origin and diversification of the Hawaiian fern genus Diellia coincides with the renewal of Hawaiian terrestrial life in the Miocene. Proc. R. Soc. London B 272 (2005) 455-460
58. Schneider H., Russell S.J., Cox C.J., Bakker F., Henderson S., Rumsey F., Barrett J., Gibby M., and Vogel J.C. Chloroplast phylogeny of asplenioid ferns based on rbcL and trnL-F spacer sequences (Polypodiidae, Aspleniaceae) and its implications for biogeography. Syst. Bot. 29 (2004) 260-274
59. Schneider H., Schuettpelz E., Pryer K.M., Cranfill R., Magallón S., and Lupia R. Ferns diversified in the shadow of angiosperms. Nature 428 (2004) 553-557
60. Schneider H., Smith A., Cranfill R., Hildebrand T., Haufler C.H., and Ranker T.A. Unraveling the phylogeny of polygrammoid ferns (Polypodiaceae and Grammitidaceae): exploring aspects of the diversification of epiphytic plants. Mol. Phylogenet. Evol. 31 (2004) 1041-1063
61. Skog J.E., Mickel J.T., Moran R.C., Volovsek M., and Zimmer E.A. Molecular studies of representative species in the fern genus Elaphoglossum (Dryopteridaceae) based on cpDNA sequences rbcL, trnL-F, and rps4-trnS. Int. J. Plant Sci. 165 (2004) 1063-1075
62. Smith A.R. Non-molecular phylogenetic hypotheses for ferns. Am. Fern J. 85 (1995) 104-122
63. Smith A.R., and Cranfill R.B. Intrafamilial relationships of the thelypteroid ferns (Thelypteridaceae). Am. Fern J. 92 (2002) 131-149
64. Smith A.R., Tuomisto H., Pryer K.M., Hunt J.S., and Wolf P.G. Metaxya lanosa, a second species in the genus and fern family Metaxyaceae. Syst. Bot. 26 (2001) 480-486
65. Stein D.B., Conant D.S., Ahearn M.E., Jordan E.T., Kirch S.A., Hasebe M., Iwatsuki K., Tan M.K., and Thomson J.A. Structural rearrangements of the chloroplast genome provide an important phylogenetic link in ferns. Proc. Natl. Acad. Sci. USA 89 (1992) 1856-1860
66. Stevenson D.W., and Loconte H. Ordinal and familial relationships of pteridophyte genera. In: Camus J.M., Gibby M., and Johns R.J. (Eds). Pteridology in Perspective (1996), Royal Botanic Gardens, Kew 435-467
67. Swofford D.L. PAUP*: Phylogenetic Analysis Using Parsimony (* and Other Methods) (2002), Sinauer Associates, Sunderland, Massachusetts
68. Tryon R. The classification of the Cyatheaceae. Contrib. Gray Herb. 200 (1970) 1-53
69. Tryon R.M., and Tryon A.F. Ferns and Allied Plants, with Special Reference to Tropical America (1982), Springer-Verlag, New York
70. White R.A., and Turner M.D. Calochlaena, a new genus of dicksonioid ferns. Am. Fern J. 78 (1988) 86-95
71. Wikström N., Kenrick P., and Vogel J.C. Schizaeaceae: a phylogenetic approach. Rev. Palaeobotan. Palynol. 119 (2002) 35-50
72. Wikström N., and Pryer K.M. Incongruence between primary sequence data and the distribution of a mitochondrial atp1 group II intron among ferns and horsetails. Mol. Phylogenet. Evol. 36 (2005) 484-493
73. Wolf P.G. Evaluation of atpB nucleotide sequences for phylogenetic studies of ferns and other pteridophytes. Am. J. Bot. 84 (1997) 1429-1440
74. Wolf P.G., Sipes S.D., White M.R., Martines M.L., Pryer K.M., Smith A.R., and Ueda K. Phylogenetic relationships of the enigmatic fern families Hymenophyllopsidaceae and Lophosoriaceae: evidence from rbcL nucleotide sequences. Plant Syst. Evol. 219 (1999) 263-270
75. Zhang X.-C., and Nooteboom H.P. A taxonomic revision of Plagiogyriaceae (Pteridophyta). Blumea 43 (1998) 401-469