Abstract
The aquatic and wetland ephemeral genus Isolepis (Cyperaceae) comprises 76 species mostly in the southern hemisphere, and especially Africa and Australasia. The latest taxonomic revision recognizes three subgenera (Fluitantes, Isolepis and Micranthae) and three sections in subgen. Isolepis. Subgen. Fluitantes, mat-forming perennial herbs typically bearing a single terminal spikelet, comprises nine species with a nearly cosmopolitan distribution except in Americas and Antarctica. Of these, I. fluitans includes infraspecific taxa from Africa–Europe and Asia–Australasia that are distinguished by the length of the involucral bract relative to the spikelet. This morphological character is also used in the key to subgen. Fluitantes that separates African–European and Asian–Australasian species. The overall morphological evidence conflicts with the species recognition of I. fluitans sensu lato and rather indicates the non-monophyly of I. fluitans, which we tested in a phylogenetic framework. Sequence data from three plastid DNA regions and nuclear ITS were analyzed using maximum parsimony, maximum likelihood, and Bayesian inference. We obtained moderately resolved phylogenies with the plastid DNA and ITS data sets. Although partially conflicting, both phylogenies rejected the monophyly of I. fluitans and instead revealed inter-continental pattern with infraspecific taxa showing close relationships with species in the subgenus within their geographic area. A revised key to species of subgenus Fluitantes is provided with the Asian–Australasian I. fluitans var. lenticularis resurrected to species rank as I. lenticularis. The phylogeny reveals a single dispersal event from Africa to Australasia, or vice versa in subgen. Fluitantes.
References
Asmussen CB, Chase MW (2001) Coding and noncoding plastid DNA in palm systematics. Amer J Bot 88:1103–1117
Baldwin BG (1992) Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from the Compositae. Molec Phylogen Evol 1:3–16. doi:10.1016/1055-7903(92)90030-K
Besnard G, Muasya AM, Russier F, Roalson EH, Salamin N, Christin PA (2009) Phylogenomics of C4 photosynthesis in sedges (Cyperaceae): multiple appearances and genetic convergence. Molec Biol Evol 26:1909–1919. doi:10.1093/molbev/msp103
Clarke LA, Rebelo CS, Gonçalves J, Boavida MG, Jordan P (2001) PCR amplification introduces errors into mononucleotide and dinucleotide repeat sequences. Mol Pathol 54:351–353
Escudero M, Valcárcel V, Vargas P, Luceño M (2010) Bipolar disjunctions in Carex: long-distance dispersal, vicariance, or parallel evolution? Flora 205:118–127. doi:10.1016/j.flora.2009.01.005
Farris JS, Källersjö M, Kluge AG, Bult C (1994) Testing significance of incongruence. Cladistics 10:315–319
Fay MF, Swensen SM, Chase MW (1997) Taxonomic affinities of Medusagyne oppositifolia (Medusagynaceae). Kew Bull 52:111–120
Felsenstein J (1985) Confidence limits on phylogenies- an approach using the bootstrap. Evolution 39:783–791
Gehrke B, Martín-Bravo S, Muasya M, Luceño M (2010) Monophyly, phylogenetic position and the role of hybridization in Schoenoxiphium Nees (Cariceae, Cyperaceae). Molec Phylogen Evol 56:380–392. doi:10.1016/j.ympev.2010.03.036
Hirahara T, Yano O, Hoshino T (2007a) Chromosome observations and chloroplast DNA sequences of a Japanese endangered species, Isolepis crassiuscula Hook. f. (Cyperaceae). Bunrui 7:23–30 (in Japanese)
Hirahara T, Katsuyama T, Hoshino T (2007b) Suprageneric phylogeny of Japanese Cyperaceae based on DNA sequences from chloroplast ndhF and 5.8 S nuclear ribosomal DNA. Acta Phytotax Geobot 58:57–68
Ito Y, Ohi-Toma T, Murata J, Tanaka N (2010) Hybridization and polyploidy of an aquatic plant, Ruppia (Ruppiaceae), inferred from plastid and nuclear DNA phylogenies. Amer J Bot 97:1156–1167. doi:10.3732/ajb.0900168
Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molec Biol Evol 30:772–780. doi:10.1093/molbev/mst010
Kelchner SA (2000) The evolution of non-coding chloroplast DNA and its application in plant systematics. Ann Missouri Bot Gard 87:482–498
Little DP, Barrington DS (2003) Major evolutionary events in the origin and diversification of the fern genus Polystichum (Dryopteridaceae). Amer J Bot 90:508–514. doi:10.3732/ajb.90.3.508
Mathews S, Lavin M, Sharrock RA (1995) Evolution of the phytochrome gene family and its utility for phylogenetic analysis of angiosperms. Ann Missouri Bot Gard 82:296–321
Muasya AM (1998) Systematics of the genus Isolepis R. Br. (Cyperaceae). PhD Thesis, University of Reading, Reading
Muasya AM, de Lange PJ (2010) Ficinia spiralis (Cyperaceae) a new genus and combination for Desmoschoenus spiralis. New Zealand J Bot 48:31–39. doi:10.1080/00288251003660703
Muasya AM, Simpson DA (2002) A monograph of the genus Isolepis R. Br. (Cyperaceae). Kew Bull 57:257–362
Muasya AM, Simpson DA, Chase MW (2001) A phylogeny of Isolepis (Cyperaceae) inferred using plastid rbcL and trnL-F sequence data. Syst Bot 26:343–353. doi:10.1043/0363-6445-26.2.342
Muasya AM, Simpson DA, Smets E (2006) Isolepis tenella, a new combination in Cyperaceae. Novon 16:89–90. doi:10.3417/1055-3177(2006)16[89:ITANCI]2.0.CO;2
Muasya AM, Simpson DA, Smets E (2007) Isolepis levynsiana, a new name for Cyperus tenellus (Cyperaceae). Novon 17:59. doi:10.3417/1055-3177(2007)17[59:ILANNF]2.0.CO;2
Muasya AM, Simpson DA, Verboom GA, Goetghebeur P, Naczi RFC, Chase MW, Smets E (2009) Phylogeny of Cyperaceae based on DNA sequence data: current progress and future prospects. Bot Rev 75:2–21. doi:10.1007/s12229-008-9019-3
Muñoz J, Felicísimo ÁM, Cabezas F, Burgaz AR, Martínez I (2004) Wind as a long-distance dispersal vehicle in the Southern Hemisphere. Science 304:1144–1147. doi:10.1126/science.1095210
Nylander JAA (2002) MrModeltest. Ver. 1.0. Program distributed by the author. Department of Systematic Zoology, Uppsala University, Uppsala. Available at: http://www.ebc.uu.se/systzoo/staff/nylander.html. Accessed 4 Apr 2012
Oxelman B, Lidén M, Berglund D (1997) Chloroplast rps16 intron phylogeny of the tribe Sileneae (Caryophyllaceae). Pl Syst Evol 206:393–410
Rambaut A, Suchard MA, Xie D, Drummond AJ (2014) Tracer. Ver. 1.6. Available at: http://beast.bio.ed.ac.uk/Tracer. Accessed 17 Sept 2014
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61:539–542. doi:10.1093/sysbio/sys029
Simpson MG (2010) Plant Systematics, 2nd edn. Elsevier Academic Press, Oxford
Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690. doi:10.1093/bioinformatics/btl446
Stamatakis A, Hoover P, Rougemont J (2008) A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 57:758–771. doi:10.1080/10635150802429642
Swofford DL (2002) PAUP: Phylogenetic analysis using parsimony (and other methods). Ver 4.0b10. Sinauer Associates, Sunderland
Taberlet P, Ludovic G, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Pl Mol Biol 17:1105–1109
WCSP (2015) World Checklist of Selected Plant Families. Facilitated by the Royal Botanic Gardens, Kew. Available at: http://apps.kew.org/wcsp/. Accessed 16 Mar 2015
Wendel JF, Doyle JJ (1998) Phylogenetic incongruence: Window into genome history and molecular evolution. In: Soltis P, Soltis D, Doyle JJ (eds) Molecular systematics of plants II. Kluwer, Dordrecht, pp 265–296
Wilson KL (1994) Cyperaceae. In: Walsh NJ, Entwistle TJ (eds) Flora of Victoria 2, Ferns and Allied Plants, Conifers and Monocotyledons. Inkata Press, Melbourne, pp 306–321
Yano O, Ikeda H, Watson MF, Rajbhandari KR, Jin X-F, Hoshino T, Muasya AM, Ohba H (2012) Phylogenetic position of the Himalayan genus Erioscirpus (Cyperaceae) inferred from DNA sequence data. Bot J Linn Soc 170:1–11. doi:10.1111/j.1095-8339.2012.01255.x
Acknowledgments
The authors thank curators of the following herbaria for arranging loans from their institutions and/or for hospitality during our recent visits: E. Cameron and D. Ranatunga (AK), E. Kapinos, L. Csiba, and T. Fulcher (K); C. Ishii (Japan) for help with DNA sequencing. We would also like to thank P. de Lange (New Zealand), P. B. Pelser (CANU), K. Wilson (NSW), J. Li (Kunming), J. Murata, H. Ikeda, and T. Ohi-Toma (TI), and T. Hoshino (OKAY) for their continuous encouragements and supports. This research was partly supported by FY 2012 Researcher Exchange Program between JSPS and RSNZ to YI, JSPS KAKENHI Grant Number 25440224 to NT, and the South African National Research Foundation (NRF) to AMM.
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List of the GenBank accessions of Isolepis used in the phylogenetic analyses of the plastid DNA and nuclear ITS sequence data sets. Sequences generated in the present study are underlined and their voucher information is provided. (DOCX 65 kb)
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Ito, Y., Viljoen, JA., Tanaka, N. et al. Phylogeny of Isolepis (Cyperaceae) revisited: non-monophyletic nature of I. fluitans sensu lato and resurrection of I. lenticularis . Plant Syst Evol 302, 231–238 (2016). https://doi.org/10.1007/s00606-015-1253-7
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DOI: https://doi.org/10.1007/s00606-015-1253-7