Reticulate evolution on a global scale: A nuclear phylogeny for New World Dryopteris (Dryopteridaceae)

Molecular Phylogenetics and Evolution

Volumn 64, Issue 3, 2012, Pages 563-581

  Sessa, Emily B ^a   Zimmer, Elizabeth A ^b   Givnish, Thomas J ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b DEPARTMENT OF PALEOBIOLOGY   (United States)

Author keywords

Divergence time estimates; Ferns; Hybridization; Neotropics; Phylogeny; Polyploidy

Indexed keywords

CHLOROPLAST DNA; PLANT DNA;

ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CELL NUCLEUS; CLASSIFICATION; DNA SEQUENCE; DRYOPTERIS; EVOLUTION; GENETICS; MOLECULAR GENETICS; NORTH AMERICA; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT;

BAYES THEOREM; BIOLOGICAL EVOLUTION; CELL NUCLEUS; DNA, CHLOROPLAST; DNA, PLANT; DRYOPTERIS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; NORTH AMERICA; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

DRYOPTERIDACEAE; DRYOPTERIS; FILICOPHYTA;

EID: 84863092138     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2012.05.009     Document Type: Article

References (100)

1. Barker F.K., Lutzoni F.M. The utility of the incongruence length difference test. Syst. Biol. 2002, 51:625-637.
2. Barrington D.S., Haufler C.H., Werth C. Hybridization, reticulation, and species concepts in the ferns. Am. Fern J. 1989, 79:55-64.
3. Beiko R., Doolittle W.F., Charlebois R. The impact of reticulate evolution on genome phylogeny. Sys. Biol. 2008, 57:844-856.
4. Bennert W., Lubienski M., Korner S., Steinberg M. Triploidy in Equisetum subgenus Hippochaete (Equisetaceae, Pteridophyta). Ann. Bot. 2005, 95:807-815.
5. Borschenius, F., 2009. FastGap 1.2. Distributed by the Author. <> (accessed 10.05.11). http://192.38.46.42/aubot/fb/FastGap_home.htm.
6. Cronn R., Small R.L., Haselkorn T., Wendel J.F. Cryptic repeated genomic recombination during speciation in Gossypium gossypiodes. Evolution 2003, 57:2475-2489.
7. Darlu P., Lecointre G. When does the incongruence length difference test fail?. Mol. Biol. Evol. 2002, 19:432-437.
8. Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214-222.
9. Drummond A.J., Ho S.Y.W., Phillips M.J., Rambaut A. Relaxed phylogenies and dating with confidence. PLoS Biol. 2006, 4:699-710.
10. Drummond, A.J., Ashton, B., Buxton, S., Cheung, M., Cooper, A., Duran, C., Field, M., Heled, J., Kearse, M., Markowitz, S., Moir, R., Stones-Havas, S., Sturrock, S., Thierer, T., Wilson, A., 2011. Geneious v5.4. <>. http://www.geneious.com/.
11. Farris J.S., Kallersjo M., Kluge A.G., Bult C. Testing significance of incongruence. Cladistics 1996, 10:315-319.
12. Fraser-Jenkins C.R. Dryopteris caucasica and the cytology of its hybrids. Fern Gaz. 1976, 11:263-267.
13. Fraser-Jenkins C.R. Dryopteris affinis: a new treatment for a complex species in the European pteridophyte flora. Willdenowia 1980, 10:107-115.
14. Fraser-Jenkins C.R. A classification of the genus Dryopteris (Pteridophyta: Dryopteridaceae). Bull. Brit. Mus. (Nat. Hist.), Bot. 1986, 14:183-218.
15. Fraser-Jenkins, C.R., 2001. Dryopteris stanley-walkeri Fras.-Jenk., the missing diploid common ancestor of D. carthusiana and D. cristata (Pteridophyta: Dryopteridaceae). In: Panda, P.C., Samant, S.S. (Eds.), Plant Diversity of the Himalaya: Prof. Y.P.S Pangtey Commemoration Volume. Gyanodaya Prakashan, Nainital, India, pp. 119-152.
16. Fraser-Jenkins C.R., Corley H.V. Dryopteris caucasica - an ancestral diploid in the male fern aggregate. Brit. Fern Gaz. 1972, 10:221-231.
17. Gastony G.J., Yatskievych G. Maternal inheritance of the chloroplast and mitochondrial genomes in Cheilanthoid ferns. Am. J. Bot. 1992, 79:716-722.
18. Geiger J.M.O., Ranker T. Molecular phylogenetics and historical biogeography of Hawaiian Dryopteris (Dryopteridaceae). Mol. Phylogenet. Evol. 2005, 34:392-407.
19. Gernhard T. The conditioned reconstructed process. J. Theor. Biol. 2008, 253:769-778.
20. Gibby M. The Dryopteris dilatata complex in Macaronesia and the Iberian Peninsula. Acta Botánica Malacitana 1983, 8:59-72.
21. Gibby M. Cytological observations on Indian subcontinent and Chinese Dryopteris and Polystichum (Pteridophyta: Dryopteridaceae). Bull. Brit. Mus. (Nat. Hist.), Bot. 1985, 14:1-42.
22. Gibby M., Walker S. Further cytogenetic studies and a re-appraisal of the diploid ancestry in the Dryopteris carthusiana complex. Brit. Fern Gaz. 1977, 11:313-324.
23. Gibby M., Jermy A.C., Rasbach H., Rasbach K., Reichstein T., Vida G. The genus Dryopteris in the Canary Islands and Azores and the description of two new tetraploid species. Bot. J. Linn. Soc. 1977, 74:251-277.
24. Givnish T.J., Sytsma K.J. Consistency, characters, and the likelihood of correct phylogenetic inference. Mol. Phylogenet. Evol. 1997, 7:320-330.
25. Goldblatt P., Johnson D.E. Index to plant chromosome numbers 1988-1989. Monogr. Syst. Bot. Missouri Bot. Gard. 1991, 40:1-238.
26. Grant V. Plant Speciation 1981, Columbia University Press. second ed.
27. Grusz A.L., Windham M.D., Pryer K.M. Deciphering the origins of apomictic polyploids in the Cheilanthes yavapensis complex (Pteridaceae). Am. J. Bot. 2009, 96:1636-1645.
28. Guindon S., Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 2003, 52:696-704.
29. Haufler C.H. Species concepts and speciation in pteridophytes. Pteridology in Perspective - Pteridophyte Symposium '95. Proceedings of the Holttum Memorial Pteridophyte Symposium 1995, 291-305. Kew Publishing, UK. G.M. Camus, M. Gibby, R.J. Johns (Eds.).
30. Haufler C.H. Genetics, phylogenetics, and biogeography: considering how shifting paradigms and continents influence fern diversity. Brittonia 2007, 59:108-114.
31. Hernandez-Hernandez V., Terrazas T., Moya C.D. The Dryopteris patula complex (Dryopteridaceae) in Mexico: morphometric analyses. Bol. de la Soc. Bot. de Mexico 2009, 85:103-112.
32. Hickok L.G., Klekowski E.J. Chromosome behavior in hybrid ferns: A reinterpretation of Appalachian Dryopteris. Am. J. Bot. 1975, 62:560-569.
33. Hipp A.L., Hall J.C., Sytstma K.J. Congruence versus phylogenetic accuracy: revisiting the incongruence length difference test. Syst. Biol. 2004, 53(1):81-89.
34. Ho S.Y.W., Phillips M.J. Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst. Biol. 2009, 58:367-380.
35. Holder M.T., Anderson J.A., Holloway A.K. Difficulties in detecting hybridization. Sys. Biol. 2001, 50:978-982.
36. Hoshizaki B.J., Wilson K.A. The cultivated species of the fern genus Dryopteris in the United States. Am. Fern J. 1999, 89:1-100.
37. Huber K.T., Oxelman B., Lott M., Moulton V. Reconstructing the evolutionary history of polyploids from multilabeled trees. Mol. Biol. Evol. 2006, 23:1784-1791.
38. Huson D.H., Bryant D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 2005, 23:254-267.
39. Hutton, C., Stein, D.B., 1992. The Common Ancestor of the Allotetraploid Ferns Dryopteris carthusiana and D. cristata: a Chloroplast DNA Analysis. Masters Thesis. Mt. Holyoke College, South Hadley, Massachusetts, USA.
40. Ishikawa H., Watano Y., Kano K., Ito M., Kurita S. Development of primer sets for PCR amplification of the pgiC gene in ferns. J. Plant Res. 2002, 115:65-70.
41. Joly S., Mclenachan P.A., Lockhart P.J. A statistical approach for distinguishing hybridization and incomplete lineage sorting. Am. Nat. 2009, 174:E54-E70.
42. Juslen A., Vare H., Wikstrom N. Relationships and evolutionary origins of polyploid Dryopteris (Dryopteridaceae) from Europe inferred using nuclear pgiC and plastid trnL-F sequence data. Taxon 2011, 60:1284-1294.
43. Kato M., Nakato N., Cheng X., Iwatsuki K. Cytotaxonomic study of ferns of Yunnan, southwestern China. Bot. Mag. (Tokyo) 1992, 105:105-124.
44. Katoh K., Misawa K., Kuma K., Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002, 30:3059-3066.
45. Laureto P.J., Barkman T.J. Nuclear and chloroplast DNA suggest a complex single origin for the threatened allopolyploid Solidago houghtonii (Asteraceae) involving reticulate evolution and introgression. Syst. Bot. 2011, 36(1):209-226.
46. Linder C.R., Rieseberg L.H. Reconstructing patterns of reticulate evolution in plants. Am. J. Bot. 2004, 91:1700-1708.
47. Lott M., Spillner A., Huber K.T., Petri A., Oxelman B., Moulton V. Inferring polyploid phylogenies from multiply-labeled gene trees. BMC Evol. Biol. 2009, 9:216.
48. Lott M., Spillner A., Huber K.T., Moulton V. PADRE: a package for analyzing and displaying reticulate evolution. Bioinformatics 2009, 25:1199-1200.
49. Maddison W.P., Knowles L.L. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 2006, 55:21-30.
50. Manton I. Problems of Cytology and Evolution in the Pteridophyta 1950, Cambridge University Press, Cambridge.
51. Mason-Gamer R.J. Reticulate evolution, introgression, and inter- tribal gene capture in an allohexaploid grass. Syst. Biol. 2004, 53:25-37.
52. McBreen K., Lockhart P.J. Reconstructing reticulate evolutionary histories of plants. Trends Plant Sci. 2006, 11:398-404.
53. Meng C., Kubatko L.S. Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence. A model. Theor. Popul. Biol. 2009, 75:35-45.
54. Mickel, J., Smith, A., 2004. Dryopteris. In Pteridophytes of Mexico. New York Botanical Garden Press, New York, USA.
55. Miller, M.A., Pfeiffer, W., Schwartz, T., 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Proceedings of the Gateway Computing Environments Workshop (GCE), 14 November 2010, New Orleans, Louisiana, pp. 1-8.
56. Montgomery, J.D., Wagner W.H., Jr., 1993. Dryopteris. In: Flora of North America Editorial Committee (Eds.), Flora of North America North of Mexico, vol. 2. Oxford University Press, New York, New York, pp. 280-288.
57. Nakato N., Kato M., Liu B.D. A cytotaxonomic study of some ferns from Jiangsu and Zhejiang Provinces, China. J. Jpn. Bot. 1995, 70:194-204.
58. Nitta J.H., Ebihara A., Ito M. Reticulate evolution in the Crepidomanes minutum species complex (Hymenophyllaceae). Am. J. Bot. 2011, 98:1-19.
59. Nixon K.C. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 1999, 15:407-414.
60. Peterson R.L., Fairbrothers D.E. Flavonols of the fern genus Dryopteris: systematic and morphological implications. Bot. Gaz. 1983, 144(1):104-109.
61. Pirie M.D., Doyle J.A. Dating clades with fossils and molecules: the case of Annonaceae. Bot. J. Linn. Soc. 2012, 169:84-116.
62. Posada D. JModelTest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 25:1253-1256.
63. Rambaut, A., Drummond, A.J., 2007. Tracer v1.4. Computer Program. <> (accessed 10.05.11). http://beast.bio.ed.ac.uk/Tracer.
64. Reyes-Jaramillo I., Camargo-Ricalde S.L., Aquiahuatl-Ramos M.A. Mycorrhizal-like interaction between gametophytes and young sporophytes of the fern Dryopteris muenchii (Filicales) and its fungal endophyte. Rev. Trop. Biol. 2008, 56:1101-1107.
65. Rieseberg L.H. Hybrid origins of plant species. Ann. Rev. Ecol. Syst. 1997, 28:359-389.
66. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
67. Russell A., Samuel R., Klejna V., Barfuss M.H.J., Rupp B., Chase M.W. Reticulate evolution in diploid and tetraploid species of Polystachya (Orchidaceae) as shown by plastid DNA sequences and low-copy nuclear genes. Ann. Bot. 2010, 106:37-56.
68. Sauquet H., Ho S.Y.W., Gandolfo M.A., Jordan G.J., Wilf P., Cantrill D.J., Bayly M.J., Bromham L., Brown G.K., Carpenter R.J., Lee D.M., Murphy D.J., Sniderman J.M.K., Udovicic F. Testing the impact of calibration of molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales). Syst. Biol. 2012, 61:289-313.
69. Sessa E.B., Zimmer E.A., Givnish T.J. Phylogeny, divergence times, and historical biogeography of New World Dryopteris (Dryopteridaceae). Am. J. Bot. 2012, 99(4):730-750.
70. Shafer A.B.A., Cullingham C.I., Cote S.D., Coltman D.W. Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America. Mol. Ecol. 2010, 19:4589-4621.
71. Sigel, E., 2008. Polyphyly of a Polyploid Species: An Inquiry into the Origin of Dryopteris campyloptera and Dryopteris dilatata (Dryopteridaceae). M.Sc. Thesis. University of Vermont, USA.
72. Sikes, D.S., Lewis, P.O., 2001. Software Manual for PAUPRat: A Tool to Implement Parsimony Ratchet Searches Using PAUP*. <> (accessed 07.04.11). http://users.iab.uaf.edu/~derek_sikes/software2.htm.
73. Simmons M.P., Ochoterena H. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 2000, 49:369-381.
74. Smith A.R. New species and new combinations of ferns from Chiapas, Mexico. Proc. Calif. Acad. Sci. 1975, 40(8):209-230.
75. Smith A.R., Pryer K., Schuettpelz E., Korall P., Schneider H., Wolf P. A classification for extant ferns. Taxon 2006, 55:705-731.
76. Soltis P.S., Soltis D.E., Savolainen V., Crane P.R., Barraclough T.G. Rate heterogeneity among lineages of tracheophytes: integration of molecular and fossil data and evidence for molecular living fossils. Proc. Nat. Acad. Sci. USA 2002, 99:4430-4435.
77. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
78. Stamatakis A., Hoover P., Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst. Biol. 2008, 57:758-771.
79. Stein D.B., Hutton C., Conant D.S., Haufler C.H., Werth C.R. Reconstructing Dryopteris " semicristata" (Dryopteridaceae): molecular profiles of tetraploids verify their undiscovered diploid ancestor. Am. J. Bot. 2010, 97(6):998-1004.
80. Swofford, D.L., 2002. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
81. Tindale M.D., Roy S.K. A cytotaxonomic survey of the Pteridophyta of Australia. Aust. Syst. Bot. 2002, 15:839-937.
82. Tsai J.L., Shieh W.C. A cytotaxonomic survey of the fern family Aspidiaceae (sensu Copeland) in Taiwan. J. Sci. Eng. 1985, 22:121-144.
83. Vogel J.C., Russell S.J., Rumsey F.J., Barrett J.A., Gibby M. Evidence for maternal transmission of chloroplast DNA in the genus Asplenium (Aspleniaceae, Pteridophyta). Bot. Acta 1998, 111:247-249.
84. Wagner, H.W., 1971. Evolution of Dryopteris in relation to the Appalachians. In: Holt, P.C. (Ed.), The Distributional History of the Biota of the Southern Appalachians, Part 2: Flora, vol. 2. Virginia Polytechnic Inst. & State Univ. Research Div. Monogr., pp. 147-192.
85. Walker S. Cytogenetic studies in the Dryopteris spinulosa complex I. Watsonia 1955, 3:193-209.
86. Walker S. Cytotaxonomic studies of some American species of Dryopteris. Am. Fern J. 1959, 49:104-112.
87. Walker S. Cytogenetic studies in the Dryopteris spinulosa complex II. Am. J. Bot. 1961, 48:607-614.
88. Walker S. Further studies in the genus Dryopteris: the origin of D. clintoniana, D. celsa, and related taxa. Am. J. Bot. 1962, 49:497-503.
89. Walker T.G. Additional cytogenetic notes on the pteridophytes of Jamaica. Trans. Roy. Soc. Edinburgh 1973, 69:109-135.
90. Werth C.R. Isozyme studies on the Dryopteris " spinulosa" complex, I: The origin of the log fern Dryopteris celsa. Syst. Bot. 1991, 16(3):446-461.
91. Wíden C.J., Britton D.M. Phloroglucinol derivative of Dryopteris tokyoensis and the missing genome in Dryopteris cristata and Dryopteris carthusiana (Dryopteridaceae). Ann. Bot. Fenn. 1985, 22:213-218.
92. Wíden C.-J., Sorsa V., Sarvela J. Dryopteris dilatata s.lat. in Europe and the island of Madeira, a chromatographic and cytological study. Acta Bot. Fenn. 1970, 91:1-30.
93. Wíden C.-J., Vida G., Euw J., Reichstein T. Die Phloroglucide von Dryopteris villarii (Bell.) Woynar und anderer Farne der Gattung Dryopteris sowie die mögliche Abstammung von D. filix-mas (L.) schott. Helv. Chim. Acta 1971, 54:2824-2850.
94. Wíden C.-J., Faden R.B., Lounasmaa M., Vida G., Euw J.V., Reichstein T. Die phloroglucide von neun Dryopteris-arten aus Kenya sowie der D. oligodonta (Desv.) Pic.-Serm. und D. " dilatata" von den Canarischen inseln. Helv. Chim. Acta 1973, 56(7):2125-2151.
95. Wíden C.-J., Fraser-Jenkins C.R., Reichstein T., Gibby M., Sarvela J. Phloroglucinol derivatives in Dryopteris sect. Fibrillosae and related taxa (Pteridophyta, Dryopteridaceae). Ann. Bot. Fenn. 1996, 33:69-100.
96. Wíden C.-J., Fraser-Jenkins C.R., Reichstein T., Sarvela J. A survey of phenolic compounds in Dryopteris and related fern genera. Part III. Ann. Bot. Fenn. 2001, 38:99-138.
97. Xiang J.Y. Chromosome numbers of 13 species in the genus Dryopteris (Dryopteridaceae) from Yunnan, China. Acta Phytotax. Sin. 2006, 44(3):304-319.
98. Xie L., Wagner W.L., Ree R.H., Berry P.E., Wen J. Molecular phylogeny, divergence time estimates, and historical biogeography of Circaea (Onagraceae) in the Northern Hemisphere. Mol. Phylogenet. Evol. 2009, 53:995-1009.
99. Yu Y., Than C., Degnan J.H., Nakhleh L. Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting. Syst. Biol. 2011, 60:138-149.
100. Zwickl, D.J., 2006. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets Under the Maximum Likelihood Criterion. Ph.D. Dissertation, The University of Texas at Austin, Austin, Texas, USA.