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Phylogenetic insights into New World Cyperus (Cyperaceae) using nuclear ITS sequences

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Abstract

We analyzed nuclear ITS sequences of 95 samples representing 85 taxa of Cyperus sensu lato under maximum likelihood and Bayesian frameworks. This work is exploratory in nature with the objectives of gaining insight into relationships among New World Cyperus and targeting problematic clades for future research. In our resulting phylogenetic hypothesis, the genera Cyperus, Kyllinga, Oxycaryum, Pycreus, and Queenslandiella were intermixed, confirming the paraphyletic nature of Cyperus as reported by other researchers. We recovered a strongly-supported clade whose members possess C4 photosynthesis. The C3/C4 split has also been previously reported based on research employing different methods of phylogenetic estimation and different molecular markers. We provide preliminary evidence that Cyperus sections Haspani, Laxiglumi, Strigosi, Thunbergiani, and Umbellati are not monophyletic. Cyperus subgenus Diclidium, which is characterized by a unique mode of spikelet shattering, is monophyletic and highly derived in our analysis, but additional taxa are needed for a more robust assessment. We discuss hypothesized relationships and taxonomic implications for several other species and species complexes.

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Literature Cited

  • Altschul, S. F., W. Gish, W. Miller, E. W. Meyers & D. J. Lipman. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403–410.

    Article  CAS  PubMed  Google Scholar 

  • Besnard, G., A. M. Muasya, F. Russier, E. H. Roalson, N. Salmin & P. A. Christin. 2009. Phylogenomics of C4 photosynthesis in sedges (Cyperaceae): multiple appearances and genetic convergence. Molecular Biology and Evolution 26: 1909–1919.

    Article  CAS  PubMed  Google Scholar 

  • Bryson, C. T. & R. Carter. 2008. The significance of Cyperaceae as weeds. In: R.F.C. Naczi and B.A. Ford (eds.), Sedges: uses, diversity, and systematics of the Cyperaceae. Monographs in Systematic Botany from the Missouri Botanical Garden 108: 15–101.

  • Carter, J. R. 1984. A systematic study of the new world species of section Umbellati of Cyperus. Ph.D. dissertation. Vanderbilt University. Nashville, Tennessee.

  • ____ & S.D. Jones. 1997. Notes on the Cyperus retroflexus complex (Cyperaceae) with three nomenclatural proposals. Rhodora 99: 319–334.

    Google Scholar 

  • Clarke, C. B. 1897. Cyperaceae. In: Thiselton-Dyer, W.T. (ed.), Flora Capensis, 7: 149–192. London, Reeve.

  • Darriba, D., G. L. Taboada, R. Doallo & D. Posada. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9(8): 772.

    Article  CAS  PubMed  Google Scholar 

  • Denton, M.F. 1978. A taxonomic treatment of the Luzulae group of Cyperus. Contributions of the University of Michigan Herbarium 11(4): 197–271.

    Google Scholar 

  • Drummond, A. J., B. Ashton, M. Cheung, J. Heled, M. Kearse, R. Moir, S. Stones-Havas, T. Thierer & A. Wilson. 2010. Geneious v 6.1.5. Website: http://www.geneious.com.

  • eMonocot Team. 2013. eMonocot Cyperaceae. Website: http://cyperaceae.e-monocot.org [accessed 23 September 2013].

  • Godfrey, R. K. & J. W. Wooten. 1979. Aquatic and wetland plants of the southeastern United States: monocotyledons. University of Georgia Press, Athens.

    Google Scholar 

  • Goetghebeur, P. 1989. Studies in Cyperaceae 9. Problems in the lectotypification and infrageneric taxonomy of Cyperus L. Bulletin de la Société Royale Botanique de Belgique 122: 103–114.

    Google Scholar 

  • ———. 1998. Cyperaceae. In: K. Kubitzki, H. Huber, P. J. Rudall, P. S. Stevens and T. Stützel (eds.), The families and genera of vascular plants, 4: 141–190. Springer-Verlag, Berlin.

  • Govaerts, R. & D. A. Simpson. 2007. World checklist of Cyperaceae (sedges). Kew Publishing, Royal Botanical Gardens, Kew, United Kingdom.

    Google Scholar 

  • Guindon, S. & O. Gascuel. 2003. A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood. Systematic Biology 52: 696–704.

    Article  PubMed  Google Scholar 

  • Haines, R. W. & K. A. Lye. 1983. The sedges and rushes of east Africa. East African Natural History Society, Nairobi.

    Google Scholar 

  • Holm, L. G., D. L. Plucknett, J. V. Pancho & J. P. Herberger. 1977. The world’s worst weeds: distribution and biology. University Press of Hawaii, Honolulu.

    Google Scholar 

  • Katoh, K., K. Misawa, K. Kuma & T. Miyata. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30(14): 3059–3066.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kern, J. H. 1974. Cyperaceae. In: C.G.G.J. van Steenis (ed.), Flora Malesiana, ser. I, 7(3): 435–753. Noordhoff, Leyden.

  • Koyama, T. 1961. Classification of the family Cyperaceae (3). Quarterly Journal of the Taiwan Museum 14: 159–194.

    Google Scholar 

  • Kükenthal, G. 1935-1936. Cyperaceae-Scirpoideae. In: A. Engler (ed.), Das Pflanzenreich, IV, 20 (Heft 101): 1–671.

  • Larridon, I., K. Bauters, M. Reynders, W. Huygh, A. M. Muasya, D. A. Simpson & P. Goetghebeur. 2013. Towards a new classification of the giant paraphyletic genus Cyperus (Cyperaceae): phylogenetic relationships and generic delimitation in C4 Cyperus. Botanical Journal of the Linnean Society 172(1): 106–126.

    Article  Google Scholar 

  • ———, M. Reynders, W. Huygh, K. Bauters, K. Van de Putte, A. M. Muasya, P. Boeckx, D. A. Simpson, A. Vrijdaghs & P. Goetghebeur. 2011a. Affinities in C3 Cyperus lineages (Cyperaceae) revealed using molecular phylogenetic data and carbon isotope analysis. Botanical Journal of the Linneaen Society 167: 19–46.

    Article  Google Scholar 

  • ———, ———, ———, ———, A. Vrijdaghs, O. Leroux, A. M. Muasya, D. A. Simpson & P. Goetghebeur. 2011b. Taxonomic changes in C3 Cyperus (Cyperaceae) supported by molecular data, morphology, embryography, ontogeny and anatomy. Plant Ecology and Evolution 144(3): 327–356.

    Article  Google Scholar 

  • Lunkai, D., G. C. Tucker & D. A. Simpson. 2010. Cyperus Linnaeus. In: W. Zhengyi, P.H. Raven, and H. Deyuan (eds). Flora of China, 23: 219–241. Missouri Botanical Garden Press, St. Louis.

  • Miller, M. A., W. Pfeiffer & T. Schwartz. 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Proceedings of the Gateway Computing Environments (GCE) Workshop, pp 1–8, 14 November 2010, New Orleans, Louisiana.

  • Muasya, A. M., D. A. Simpson & M. W. Chase. 2001. Generic relationships and character evolution on Cyperus s.l. (Cyperaceae). Systematics and Geography of Plants 71: 539–544.

    Article  Google Scholar 

  • ———, ——— & ———. 2002. Phylogenetic relationships in Cyperus L. s.l. (Cyperaceae) inferred from plastid DNA sequence data. Botanical Journal of the Linneaen Society 138: 145–153.

  • ———, ———, ——— & A. Culham. 1998. An assessment of suprageneric phylogeny in Cyperaceae using rbcL DNA sequences. Plant Systematics and Evolution 211: 257–271.

  • ____, ____, G. A. Verboom, P. Goetghebeur, R. F. C. Naczi, M. W. Chase & E. Smets. 2009a. Phylogeny of Cyperaceae based on DNA sequence data: current progress and future prospects. Botanical Review 75: 2–21.

  • ———, A. Vrijdaghs, D. A. Simpson, M. W. Chase, P. Goetghebeur & E. Smets. 2009b. What is a genus in Cypereae?: phylogeny, character homology assessment and generic circumscription in Cypereae. Botanical Review 75: 52–66.

  • Pedersen, T. M. 1972. Cyperus laetus Presl and Cyperus rigens Presl, two badly understood South American sedges, with notes on some related species. Darwiniana 17: 527–547.

    Google Scholar 

  • Rambaut, A. 2006-2009. Fig Tree. Tree Figure Drawing Tool Ver. 1.3.1. Institute of Evolutionary Biology, University of Edinburgh.

  • ——— & A. J. Drummond. 2007. Tracer v. 1.5. Website: http://beast.bio.ed.ac.uk/Tracer.

  • Reynders, M., A. Vrijdaghs, I. Larridon, W. Huygh, O. Leroux, A. M. Muasya & P. Goetghebeur. 2010. The Cypereae radiation: Pycreus highlighted (Cyperaceae). Scripta Botanica Belgica 46: 445.

    Google Scholar 

  • Rikli, M. 1895. Beiträge zur vergleichenden anatomie der Cyperaceen mit besonderer berücksichtigung der inneren parenchymscheide. Jahrbücher für Wissenschaftliche Botanik 27: 485–580.

    Google Scholar 

  • Ronquist, F. & J. P. Huelsenbeck. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–1574.

    Article  CAS  PubMed  Google Scholar 

  • Schippers, P., S. J. T. Borg & J. J. Bos. 1995. A revision of the infraspecific taxonomy of Cyperus esculentus (yellow nutsedge) with an experimentally evaluated character set. Systematic Botany 20(4): 461–481.

    Article  Google Scholar 

  • Simpson, D. A., A. M. Muasya, M. V. Alves, J. J. Bruhl, S. Dhooge, M. W. Chase, C. A. Furness, K. Ghamkhar, P. Goetghebeur, T. R. Hodkinson, A. D. Marchant, A. A. Reznicek, R. Nieuwborg, E. H. Roalson, E. Smets, J. R. Starr, W. W. Thomas, K. L. Wilson & X. Zhang. 2007. Phylogeny of Cyperaceae based on DNA sequence data – a new rbcL analysis. Aliso 23: 72–83.

    Article  Google Scholar 

  • Siripun, K.C. & E. E. Schilling. 2006. Molecular confirmation of the hybrid origin of Eupatorium godfreyanum (Asteraceae). American Journal of Botany 93(2): 319–325.

    Article  CAS  PubMed  Google Scholar 

  • Small, J. K. 1933. Manual of the southeastern flora. University of North Carolina Press, Chapel Hill.

    Google Scholar 

  • Stamatakis, A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22(21): 2688–2690.

    Article  CAS  PubMed  Google Scholar 

  • Sukumaran J. & M. T. Holder. 2010. DendroPy: A Python library for phylogenetic computing. Bioinformatics. 26: 1569–1571.

    Article  CAS  PubMed  Google Scholar 

  • Sun, Y., D. Z. Skinner, G. H. Liang & S. H. Hulbert. 1994. Phylogenetic analysis of Sorghum and related taxa using internal transcribed spacer of nuclear ribosomal DNA. Theoretical and Applied Genetics 89: 26–32.

    Article  CAS  PubMed  Google Scholar 

  • Tucker, G. C. 1984. Taxonomic notes on two common neotropical species of Cyperus (Cyperaceae). Sida 10(4): 298–307.

    Google Scholar 

  • ———. 2002. Kyllinga Rottbøll. In: Flora of North America Editorial Committee (eds.), Flora of North America North of Mexico, 23: 193–194. Oxford University Press, New York.

  • Tucker, G. C., B. G. Marcks & J. R. Carter. 2002. Cyperus Linnaeus. In: Flora of North America Editorial Committee (eds.), Flora of North America North of Mexico, 23: 141–191. Oxford University Press, New York.

  • Wunderlin, R. P. & B. F. Hansen. 2003. Guide to the vascular plants of Florida, 2nd ed. University Press of Florida, Gainesville.

    Google Scholar 

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Acknowledgments

Field work for this research was supported by Coypu Foundation and Louisiana Department of Wildlife and Fisheries. The senior author would like to thank David Rosen for assistance and companionship in the field while working in Texas. He would also like to thank Gabriella Lopez and Ricardo Vanni of CTES for hosting him while in Corrientes, Argentina. Without them, his field work in Argentina would not have been possible. Randy Mears assisted R.C. with fieldwork in southern Florida and provided us with material of Cyperus planifolius. Jerry Abbott and Kurt Neubig of FLAS kindly provided silica-dried material of several taxa for this study. Vinson Doyle provided invaluable help with the Bayesian analysis and with SumLabels and his assistance is greatly appreciated. Patti Hardouin assisted generously with preparation of figures. Maria Reid proof read the manuscript. Fred Sheldon reviewed an early version of this manuscript, and we appreciate his input. Isabel Larridon and Muthama Muasya provided helpful reviews that greatly improved this manuscript. Janelle Burke worked closely with C.S.R. to complete preparation of this manuscript for publication, and her help and patience is greatly appreciated.

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  1. Louisiana State University Herbarium, Rm. A257 Life Sciences Annex, Baton Rouge, LA, 70803, USA

    Christopher S. Reid & Lowell E. Urbatsch

  2. Herbarium, Biology Department, 2035 Bailey Science Center, Valdosta State University, 1500 North Patterson St., Valdosta, GA, 31698-0015, USA

    Richard Carter

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  1. Christopher S. Reid
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Correspondence to Christopher S. Reid.

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Reid, C.S., Carter, R. & Urbatsch, L.E. Phylogenetic insights into New World Cyperus (Cyperaceae) using nuclear ITS sequences. Brittonia 66, 292–305 (2014). https://doi.org/10.1007/s12228-014-9324-6

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