Species diversity and reticulate evolution in the Asplenium normale complex (Aspleniaceae) in China and adjacent areas

Taxon

Volumn 62, Issue 4, 2013, Pages 673-687

  Chang, Yanfen ^a,b,f   Li, Jie ^a   Lu, Shugang ^c   Schneider, Harald ^d,e  

^a CHINESE ACADEMY OF SCIENCES   (China)

^b KEY LABORATORY OF TROPICAL FOREST ECOLOGY   (China)

^c YUNNAN UNIVERSITY   (China)

^d DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

^e INSTITUTE OF BOTANY   (China)

^f UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Aspleniaceae; Asplenium; Chloroplast DNA; Genome size; PgiC; Polyploidy; Reticulation; Taxonomy

Indexed keywords

CHLOROPLAST; CLASSIFICATION; DATA ACQUISITION; FERN; GENOME; PHYLOGENETICS; PLASTID; PLOIDY; PTERIDOPHYTE; SPECIES DIVERSITY; TAXONOMY;

CHINA;

EID: 84883030503     PISSN: 00400262     EISSN: None     Source Type: Journal    
DOI: 10.12705/624.6     Document Type: Article

References (83)

1. Akaike, H. 1974. A new look at the statistical model identification. I. E. E. E. Trans. Automatic Control 19: 716-723. http://dx.doi.org/10.1109/TAC.1974.110 0705
2. Bainard, J.D., Henry, T.A., Bainard, L.D. & Newmaster, S.G. 2011. DNA content variation in monilophytes and lycophytes: Large genomes that are not endopolyploid. Chromosome Res. 19: 763-775. http://dx.doi.org/10.1007/s10577-011-9228-1
3. Barrington, D.S. & Paris, C.A. 1986. Systematic inferences from spore and stomata size in the ferns. Amer. Fern J. 76: 149-159. http://dx.doi.org/10.2307/1547723
4. Boykin, L.M., Armstrong, K.F., Kubatko, L. & de Barro, P. 2012. Species delimitation and global biosecurity. Evol. Bioinf. 8: 1-37. http://dx.doi.org/10.4137/EBO.S8532
5. Brysting, A.K., Oxelman, B., Huber, K.T., Moulton, V. & Broch-mann, C. 2007. Untangling complex histories of genome mergings in high polyploids. Syst. Biol. 56: 467-476. http://dx.doi.org/10.1080/10635150701424553
6. Brysting, A.K., Mathiesen, C. & Marcussen, T. 2011. Challenges in polyploid phylogenetic reconstruction: A case story from the arctic-alpine Cerastium alpinum complex. Ta x o n 60: 333-347.
7. Clement, M., Posada, D. & Crandall, K. 2000. TCS: A computer program to estimate gene genealogies. Molec. Ecol. 9: 1657-1660. http://dx.doi.org/10.1046/j.1365-294x.2000.01020.x
8. Dolezel, J., Greilhuber, J. & Suda, J. 2007. Estimation of nuclear DNA content in plants using flow cytometry. Nat. Protoc. 2: 2233-2244. http://dx.doi.org/10.1038/nprot.2007.310
9. Doyle, J.J. & Doyle, J.L. 1987. A rapid DNA isolation procedure for small quantities of fresh tissue. Phytochemistry 19: 11-15.
10. Doyle, J.J., Doyle, J.L., Rauscher, J.T. & Brown, A.H.D. 2003. Dip-loid and polyploid reticulate evolution throughout the history of the perennial soybeans (Glycine subgenus Glycine). New Phytol. 161: 121-132. http://dx.doi.org/10.1046/j.1469-8137.2003.00949.x
11. Dyer, R.J., Savolainen, V. & Schneider, H. 2012. Apomixis and reticulate evolution in the Asplenium monanthes fern complex. Ann. Bot. (Oxford) 110: 1515-1529. http://dx.doi.org/10.1093/aob/mcs202
12. Ebihara, A., Nitta, J.H. & Ito, M. 2010. Molecular species identification with rich floristic sampling: DNA barcoding the pteridophyte flora of Japan. PloS ONE 5: e15136. http://dx.doi.org/10.1371/jour nal.pone.0015136
13. Gastony, G.J. & Yatskievych, G. 1992. Maternal inheritance of the chloroplast and mitochondrial genomes in cheilanthoid ferns. Amer. J. Bot. 79: 716-722. http://dx.doi.org/10.2307/2444887
14. Ghatak, J. 1977. Biosystematic survey of pteridophytes from Shevaroy Hills, South India. Nucleus 20: 105-108.
15. Glez-Pena, D., Gomez-Blanco, D., Rebioro-Jato, M., Fdez-Riverola, F. & Posada, D. 2010. ALTER: Program-oriented conversions of DNA and protein aligments. Nucl. Acids Res. 38: W14-W18. http://dx.doi.org/10.1093/nar/gkq321
16. Grusz, A.L., Windham, M.D. & Pryer, K.M. 2009. Deciphering the origins of apomictic polyploids in the Cheilanthes yavapensis complex (Pteridaceae). Amer. J. Bot. 96: 1636-1645. http://dx.doi.org/10.3732/ajb.0900019
17. Guindon, S., Dufayard, J.F., Lefort, V., Anisimova, M., Hordijk, W. & Gascuel, O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Syst. Biol. 59: 307-321. http://dx.doi.org/10.1093/sysbio/syq010
18. Hauk, W.D. & Haufler, C.H. 1999. Isozyme variability among cryptic species of Botrychium subgenus Botrychium (Ophioglossaceae). Amer. J. Bot. 86: 614-633. http://dx.doi.org/10.2307/2656570
19. Herrero, A., Pajarón, S. & Prada, C. 2001. Isozyme variation and genetic relationships among taxa in the Asplenium obovatum group (Aspleniaceae, Pteridophyta). Amer. J. Bot. 88: 2040-2050. http://dx.doi.org/10.2307/3558430
20. Huber, K., Oxelman, B., Lott, M. & Moulton, V. 2006. Reconstructing the evolutionary history of polyploids from multi-labelled trees. Molec. Biol. Evol. 23: 1784-1791. http://dx.doi.org/10.1093/molbev/msl045
21. Huelsenbeck, J.P. & Ronquist, F. 2001. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17: 754-755. http://dx.doi.org/10.1093/bioinformatics/17.8.754
22. Ishikawa, H., Watano, Y., Kano, K., Ito, M. & Kurita, S. 2002. Development of primer sets for PCR amplification of the pgiC gene in ferns. J. Pl. Res. 115: 65-70. http://dx.doi.org/10.1007/s10265020 0010
23. Ito, H. 1972. A new variety of Asplenium normale. J. Jap. Bot. 47: 186-187.
24. Iwashina, T. 2000. The structure and distribution of the flavonoids in plants. J. Pl. Res. 113: 287-299. http://dx.doi.org/10.1007/PL0 0013940
25. Iwashina, T. & Matsumoto, S. 1994. Flavonoid variation and evolution in Asplenium normale and related species (Aspleniaceae). J. Pl. Res. 107: 275-282. http://dx.doi.org/10.1007/BF02344255
26. Iwatsuki, K. 1995. Flora of Japan. Tokyo: Kodansha.
27. Juslen, A., Vare, H. & Wikstrom, N. 2011. Relationships and evolutionary origins of polyploid Dryopteris (Dryopteridaceae) from Europe inferred using nuclear pgiC and plastid trnL-F sequence data. Taxon 60: 1284-1294.
28. Kamiya, K., Gan, Y.Y., Lum, S.K.Y., Khoo, M.S., Chua, S.C. & Faizu, N. 2011. Morphological and molecular evidence of natural hybridization in Shorea (Dipterocarpaceae). Tree Genet. Genomes 7: 297-306. http://dx.doi.org/10.10 07/s11295-010 - 0332-8
29. Kurata, S. 1963. Notes on Japanese ferns (29). J. Geobot. 11: 98-102.
30. Lin, Y.X. 1999. Flora Reipublicae Popularis Sinicae, vol. 4(2). Beijing: Science Press.
31. Lin, Y.X. & Viane, R. 2012. Flora of China, vol. 2, Aspleniaceae. Beijing: Science Press; St. Louis: Missouri Botanical Garden Press.
32. Lott, M., Spillner, A., Huber, K.T. & Moulton, V. 2009. PADRE: A package for analyzing and displaying reticulate evolution. Bioin-formatics 25: 1199-1200. http://dx.doi.org/10.1093/bioinformatics/btp133
33. Lovis, J.D. 1978. Evolutionary patterns and processes in ferns. Advances Bot. Res. 4: 229-415. http://dx.doi.org/10.1016/S0065 -2296(08)60371-7
34. Masters, D.C., Fan, V. & Ross, H.A. 2011. Species delimitation-a geneious plugin for the exploration of species boundaries. Molec. Ecol. Resources 11: 154-157. http://dx.do i.org/10.1111/j.1755-0998.2010.02896.x
35. Masuyama, S., Yatabe, Y., Murakami, N. & Watano, Y. 2002. Cryptic species in the fern Ceratopteris thalictroides (L.) B r o n g n. (Parkeri aceae). I. Molecular analyses and crossing tests. J. Pl. Res. 115: 87-97. http://dx.doi.org/10.1007/s10265020 0013
36. Matsumoto, S. 1975. Cyto-ecological study of three types of Asplenium normale. J. Nippon Fernist Club 2: 338-340.
37. Matsumoto, S. & Nakaike, T. 1988. Chromosome numbers of some ferns in Kathmandu Nepal. Pp. 177-185 in: Watanabe, M. & Malla, S.B. (ed.): Cryptogams of the Himalayas, vol. 1. Tsukuba: Department of Botany, National Science Museum.
38. Matsumoto, S., Iwashina, T., Kitajima, J. & Mitsuta, S. 2003. Evidence by flavonoid markers of four natural hybrids among Asplenium normale and related species (Aspleniaceae) in Japan. Biochem. Syst. Ecol. 31: 51-58. http://dx.doi.org/10.1016/S0305-1978(02)0 0062-5
39. Murakami, N., Nogami, S., Watanabe, M. & Iwatsuki, K. 1999. Phy-logeny of Aspleniaceae inferred from rbcL nucleotide sequences. Amer. Fern J. 89: 232-243. http://dx.doi.org/10.2307/1547233
40. Nakaike, T. 1992. New Flora of Japan: Pteridophyta, revised & enlarged. Tokyo: Shibundo.
41. Paris, C.A., Wagner, F.S. & Wagner, W.H., Jr. 1989. Cryptic species, species delimitation, and taxonomic practice in homosporous ferns. Amer. Fern J. 79: 46-54. http://dx.doi.org/10.2307/1547159
42. Perrie, L.R. & Brownsey, P.J. 2005. Insights into the biogeography and polyploid evolution of New Zealand Asplenium from chloroplast DNA sequence data. Amer. Fern J. 95: 1-21. http://dx.doi.org/10.1640/0002-8444(2005)095%5B0001:IITBAP%5D2.0.CO;2
43. Perrie, L.R., Shepherd, L.D., de Lnage, P.J. & Brownsey, P.J. 2010. Parallel polyploid speciation: Distinct sympatric gene-pools of recurrently derived allo-octoploid Asplenium ferns. Molec. Ecol. 19: 2916-2932. http://dx.doi.org/10.1111/j.1365-294X.2010.04705.x
44. Pinter, I., Bakker, F., Barrett, J., Cox, C., Gibby, M., Henderson, S., Morgan-Richards, M., Rumsey, F., Russell, S., Trewick, S., Schneider, H. & Vogel, J. 2002. Phylogenetic and biosystematic relationships in four highly disjunct polyploid complexes in the subgenera Ceterach and Phyllitis in Asplenium (Aspleniaceae). Organisms Diversity Evol. 2: 29 9-311. http://dx.doi.org/10.1078/1439-6092-00050
45. Pons, J., Barraclough, T.G., Gomez-Zurita, J., Cardoso, A., Duran, D.P., Hazell, S., Kamoun, S., Sumlin, W.D. & Vogler, A.P. 2006. Seuqence-based species delimitation for the DNA taxonomy of undescribed insests. Syst. Biol. 55: 595-609. http://dx.doi.org/10.1080/1063515060 0852011
46. Posada, D. 2008. jModelTest: Phylogenetic model averaging. Molec. Biol. Evol. 25: 1253-1256. http://dx.doi.org/10.1093/molbev/msn083
47. Redondo, N., Horjales, M. & Blanco, A. 1999. Nuclear DNA amounts and spores in Aspleniaceae: Asplenium L. Phyllitis Hill and Ceterach Willd. Nova Acta Ci. Compostelana, Biol. 9: 99-107.
48. Reichstein, T. 1981. Hybrids in European Aspleniaceae (Pteridophyta). Bot. Helv. 91: 89-139.
49. Rieseberg, L.H. 1995. The role of hybridization in evolution: Old wine in new skins. Amer. J. Bot. 82: 944-953. http://dx.doi.org/10.2307/2445981
50. Rodrigo, A.G., Bertels, F., Heled, J., Noder, R., Shearman, H. & Tsai, O.P. 2008. The perils of plenty: What are we going to do with these genes? Philos. Trans., Ser. B. 363: 3893-3902.
51. Rosenberg, N.A. 2007. Statistical tests for taxonomic distinctiveness from observation of monophyly. Evolution 61: 317-323. http://dx.doi.org/10.1111/j.1558-5646.2007.00023.x
52. Ross, H.A., Murugan, S. & Li, W.L.S. 2008. Testing the reliability of genetic methods of species identification via simulations. Syst. Biol. 57: 216-230. http://dx.doi.org/10.1080/10635150802032990
53. Rozas, J., Sanchez-DelBarrio, J.C., Messeguer, X. & Rozas, R. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497. http://dx.doi.org/10.1093/bioinformatics/btg359
54. Russell, A., Samuel, R., Klejna, V., Barfuss, M.H., Rupp, B. & Chase, M.W. 2010. Reticulate evolutionin in diploid and tetraploid species of Polystachya (Orchidaceae) as shown by plastid DNA sequences and low-copy nuclear genes. Ann. Bot. (Oxford) 106: 37-56. http://dx.doi.org/10.1093/aob/mcq092
55. Sang, T. 2002. Utility of low copy nuclear gene sequences in plant phylogenetics. Crit. Rev. Biochem. Molec. Biol. 37: 121-147. http://dx.doi.org/10.1080/104 09230290771474
56. Sang, T. & Zhong, Y. 2000. Testing hybridization hypotheses based on incongruent gene trees. Syst. Biol. 49: 422-434. http://dx.doi.org/10.1080/10635159950127321
57. Schneider, H., Russell, S.J., Cox, C.J., Bakker, F., Henderson, S., Rumsey, F., Barrett, J., Gibby, M. & Vogel, J.C. 2004. Chlo-roplast phylogeny of asplenioid ferns based on rbcL and trnL-F spacer sequences (Polypodiidae, Aspleniaceae) and its implications for biogeography. Syst. Bot. 29: 260-274. http://dx.doi.org/10.1600/036364404774195476
58. Schneider, H., Ranker, T.A., Russell, S.J., Cranfill, R., Geiger, J.M.O., Aguraiuja, R., Wood, K.R., Grundmann, M., Klober-danz, K. & Vogel, J.C. 2005. Origin of the endemic fern genus Diellia coincides with the renewal of Hawaiian terrestrial life in the Miocene. Proc. Roy. Soc. London, Ser. B., Biol. Sci. 272: 455-460. http://dx.doi.org/10.1098/rspb.2004.2965
59. Sessa, E.B., Zimmer, E.A. & Givnish, T.J. 2012. Reticulate evolution on a global scale: A nuclear phylogeny for New World Dryopteris (Dryopteridaceae). Molec. Phylogen. Evol. 64: 563-581. http://dx.doi.org/10.1016/j.ympev.2012.05.009
60. Smedmark, J.E.E., Eriksson, T. & Bremer, B. 2005. Allopolyploid evolution in Geinae (Colurieae: Rosaceae)-Buliding reticulate species trees from bifurcating gene trees. Organisms Diversity Evol. 5: 275-283. http://dx.doi.org/10.1016/j.ode.2004.12.003
61. Sprunt, S.V., Schneider, H., Watson, L.E., Russell, S.J., Navarro-Gomez, A. & Hickey, R.J. 2011. Exploring the molecular phylogeny and biogeography of Pleopeltis polypodioides (Polypodiacae, Polypodiales) inferred from plastic DNA sequences. Syst. Bot. 36: 862-869. http://dx.doi.org/10.1600/036364411X604886
62. Staden, R., Beal, K.F. & Bonfield, J.K. 2000. The Staden Package, 1998. Methods Molec. Biol. 132: 115-130.
63. Suda, J., Krahulcová, A., Trávnícek, P. & Krahulec, F. 2006. Ploidy level versus DNA ploidy level: An appeal for consistent terminolog y. Ta x o n 55: 447-450. http://dx.doi.org/10.2307/25065591
64. *: Phylogenetic Analysis using parsimony (*and other methods), version 4.0 beta. Sunderland Massachusetts: Sinauer.
65. Taberlet, P., Gielly, L., Pautou, G. & Bouvet, J. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Pl. Molec. Biol. 17: 1105-1109. http://dx.doi.org/10.1007/BF00037152
66. Tamura, K., Dudley, J., Nei, M. & Kumar, S. 2007. MEGA4: morlecular evolutionary genetics analysis (MEGA) software version 4.0. Molec. Biol. Evol. 24: 1596-1599. http://dx.doi.org/10.1093/molbev/msm092
67. Tardieu-Blot, M.L. 1958. Flore de Madagascar et des Comores, vol. 5. Paris: Firmin-Didot.
68. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. & Higgins, D.G. 1997. The Clustal X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res. 24: 4876-4882. http://dx.doi.org/10.1093/nar/25.24.4876
69. Trewick, S.A., Morgan-Richards, M., Russell, S.J., Henderson, S., Rumsey, F.J., Pinter, I., Barrett, J.A., Gibby, M. & Vogel, J.C. 2002. Polyploidy, phylogeography and Pleistocene refugia of the rockfern Asplenium ceterach: Evidence from chloroplast DNA. Molec. Ecol. 11: 2003-2012. http://dx.doi.org/10.1046/j.1365-294X.2002.01583.x
70. Van den Heede, C.G., Viane, R.L.L. & Chase, M.W. 2003. Phylo-genetic analysis of Asplenium subgenus Ceterach (Pteridophyta: Aspleniaceae) based on plastid and nuclear ribosomal ITS DNA sequences. Amer. J. Bot. 90: 481-495. http://dx.doi.org/10.3732/ajb.90.3.481
71. Vogel, J.C., Russell, S.J., Rumsey, F.J., Barrett, J.A. & Gibby, M. 1998. Evidence for maternal transmission of chloroplast DNA in the genus Asplenium (Aspleniaceae, Pteridophyta). Bot. Acta 111: 247-249.
72. Wagner, W.H. 1954. Reticulate evolution in the Appalachian Asplenium. Evolution 8: 103-118. http://dx.doi.org/10.2307/2405636
73. Wagner, W.H. 1993. New species of Hawaiian pteridophytes. Contr. Univ. Michigan Herb. 19: 63-82.
74. Wang, L., Wu, Z.Q., Bystriakova, N., Ansell, S.W., Xiang, Q.P., Heinrichs, J., Schneider, H. & Zhang, X.C. 2011. Phylogeography of the Sino-Himalayan fern Lepisorus clathratus on "the roof of the world". PLoS ONE 6: e25896. http://dx.doi.org/10.1371/journal.pone.0025896
75. Wang, L., Schneider, H., Wu, Z.Q., He, L.J., Zhang, X.C. & Xiang, Q. P. 2012. Indehiscent sporangia enable the accumulation of local fern diversity at the Qinghai-Tibetan Plateau. B. M. C. Evol. Biol. 12: 158. http://dx.doi.org/10.1186/1471-2148-12-158
76. Wang, Z.R. 1988. A preliminary report on the cytology of some species of Asplenium from China. Pp. 133-134 in: Shing, K.H. & Kramer K.U. (ed.), Proceedings of the International Symposium on Systematic Pteridology. Beijing: China Science and Technology Press.
77. Weng, R.F. & Qiu, S.P. 1988. Chromosome counts of some ferns from Zhejiang. Invest. Stud. Nat. 8: 43-52.
78. Werth, C.R., Guttman, S.I. & Eshbaugh, W.H. 1985. Electrophoretic evidence of reticulate eovlution in the Appalachian Asplenium complex. Syst. Bot. 10: 184-192. http://dx.doi.org/10.2307/2418344
79. Yatabe, Y. & Murakami, N. 2003. Recognition of cryptic species in the Asplenium nidus complex using molecular data-a progress report. Te lope a 10: 487-496.
80. Yatabe, Y., Masuyama, S., Darnaedi, D. & Murakami, N. 2001. Molecular systematics of the Asplenium nidus complex from Mt. Halimun National Park, Indonesia: Evidence for reproductive isolation among three sympatric rbcL sequence types. Amer. J. Bot. 88: 1517-1522. http://dx.doi.org/10.2307/3558459
81. Yatabe, Y., Shonohara, W., Matsumoto, S. & Murakami, N. 2009. Patterns of hybrid formation among cryptic species of bird-nest fern, Asplenium nidus complex (Aspleniaceae), in West Malesia. Bot. J. Linn. Soc. 160: 42-63. http://dx.doi.org/10.1111/j.1095 - 8339.2009.0 0 96 4.x
82. Young, N.D. & Healy, J. 2003. GapCoder automates the use of indel characters in phylogenetic analysis. B. M. C. Bioinf. 4: 487-496.
83. Zhu, W.M. 1992. Taxonomic notes on some pteridophytes from Yunnan (mainly Dulongjiang and neighbouring regions). Acta Bot. Yunnan. 5: 34-58.