Exploring evolutionary dynamics of nrDNA in Carex subgenus Vignea (cyperaceae)

Systematic Botany

Volumn 33, Issue 3, 2008, Pages 514-524

  King, Matthew G ^a   Roalson, Eric H ^a  

^a WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

Carex; ETS; Incomplete concerted evolution; Incomplete lineage sorting; ITS; NrDNA

Indexed keywords

CAREX; CYPERACEAE;

EID: 51549102585     PISSN: 03636445     EISSN: 15482324     Source Type: Journal    
DOI: 10.1600/036364408785679860     Document Type: Article

References (56)

1. Altekar, G., S. Dwarkadas, J. P. Huelsenbeck, and F. Ronquist. 2004. Parallel Metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics (Oxford, England) 20: 407-415.
2. Álvarez, I. and J. F. Wendel. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29: 417-434.
3. Bailey, C. D., T. G. Carr, S. A. Harris, and C. E. Hughes. 2003. Characterization of angiosperm nrDNA polymorphism, paralogy, and pseudogenes. Molecular Phylogenetics and Evolution 29: 435-455.
4. Baldwin, B. G. 1992. Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from the Compositae. Molecular Phylogenetics and Evolution 1: 3-16.
5. Baldwin, B. G. and S. Markos. 1998. Phylogenetic utility of the external transcribed spacer (ETS) of 18S 26S rDNA: Congruence of ETS and ITS trees of Calycadenia (Compositae). Molecular Phylogenetics and Evolution 10: 449-463.
6. Baldwin, B. G., M. J. Sanderson, J. M. Porter, M. F. Wojciechowski, C. S. Campbell, and M. J. Donoghue. 1995. The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Annals of the Missouri Botanical Garden 82: 247-277.
7. Buckler, E. S. and T. P. Holtsford. 1996. Zea ribosomal repeat evolution and substitution patterns. Molecular Biology and Evolution 13: 623-632.
8. Buckler, E. S., A. Ippolito, and T. P. Holtsford. 1997. The evolution of ribosomal DNA: divergent paralogues and phylogenetic implications. Genetics 145: 821-832.
9. Campbell, C. S., M. F. Wojciechowski, B. G. Baldwin, L. A. Alice, and M. J. Donoghue. 1997. Persistent nuclear ribosomal DNA sequence polymorphism in the Amelanchier agamic complex (Rosaceae). Molecular Biology and Evolution 14: 81-90.
10. Cayouette, J. and P. M. Catling. 1992. Hybridization in the genus Carex with special reference to North America. Botanical Review 58: 351-440.
11. Cronn, R. C., X. Zhao, A. H. Paterson, and J. F. Wendel. 1996. Polymorphism and concerted evolution in a tandemly repeated gene family: 5S ribosomal DNA in diploid and allopolyploid cottons. Journal of Molecular Evolution 42: 685-705.
12. Denduangboripant, J. and Q. C. B. Cronk. 2000. High intraindividual variation in internal transcribed spacer sequences in Aeschynanthus (Gesneriaceae) implications for phylogenetics. Proceedings of the Royal Society of London. Series B. Biological Sciences 267: 1407-1415.
13. Dobes, C., T. Mitchell-Olds, and M. A. Koch. 2004. Intraspecific diversification in North American Boechera stricta (= Arabis drummondii), Boechera xdivaricarpa, and Boechera holboellii (Brassicaceae) inferred from nuclear and chloroplast molecular markers - An integrative approach. American Journal of Botany 91: 2087-2101.
14. Doyle, J. J. and J. I. Davis. 1998. Homology in molecular phylogenetics: a parsimony perspective. Pp. 101-131 in Molecular systematics of plants II: DNA Sequencing, eds. D. E. Soltis, P. S. Soltis, and J. J. Doyle. Boston: Kluwer Academic.
15. Ford, B. A., M. Iranpour, F. C. Naczi, J. R. Starr, and C. A. Jerome. 2006. Phylogeny of Carex subg. Vignea (Cyperaceae) based on non-coding nrDNA sequence data. Systematic Botany 31: 70-82.
16. Fuertes-Aguilar, J., J. A. Rossello, and G. Nieto Feliner. 1999. Nuclear ribosomal DNA (nrDNA) concerted evolution in natural and artificial hybrids of Armeria (Plumbaginaceae). Molecular Ecology 8: 1341-1346.
17. Gernandt, D. S. and A. Liston. 1999. Internal transcribed spacer region evolution in Larix and Pseudotsuga (Pinaceae). American Journal of Botany 86: 711-723.
18. Hamby, R. K. and E. A. Zimmer. 1992. Ribosomal RNA as a phylogenetic tool in plant systematics. Pp. 50-91 in Molecular systematics of plants, eds. P. S. Soltis, D. E. Soltis, J. J. Doyle. New York: Chapman & Hall.
19. Hartmann, S., J. D. Nason, and D. Bhattacharya. 2001. Extensive ribosomal DNA genic variation in the columnar cactus Lophocereus. Journal of Molecular Evolution 53: 124-134.
20. Hendrichs, M., S. Michalski, D. Begerow, F. Oberwinkler, and F. H. Hellwig. 2004. Phylogenetic relationships in Carex, subgenus Vignea (Cyperaceae), based on ITS sequences. Plant Systematics and Evolution 246: 109-125.
21. Hershkovitz, M. A., E. A. Zimmer, and W. J. Hahn. 1999. Ribosomal DNA sequences and angiosperm systematics. Pp. 268-326 in Molecular Systematics and Plant Evolution, ed. P. M. Hollingsworth, R. M. Bateman, and R. J. Gornall. London: Taylor & Francis.
22. Hillis, D. M., C. Moritz, C. A. Porter, and R. J. Baker. 1991. Evidence of biased gene conversion in concerted evolution of ribosomal DNA. Science 251: 308-310.
23. Hipp, A. L., A. A. Reznicek, P. E. Rothrock, and J. A. Weber. 2006. Phylogeny and classification of Carex section Ovales (Cyperaceae). International Journal of Plant Sciences 167: 1029-1048.
24. Huelsenbeck, J. P., F. Ronquist, R. Nielsen, and J. P. Bollback. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294: 2310-2314.
25. Hughes, C. E., C. D. Bailey, and S. A. Harris. 2002. Divergent and reticulate species relationships in Leucaena (Fabaceae) inferred from multiple data sources: insights into polyploid origins and nrDNA polymorphism. American Journal of Botany 89: 1057-1073.
26. Johnson, L. A. and D. E. Soltis. 1995. Phylogenetic inference in Saxifragaceae sensu stricto and Gilia (Polemoniaceae) using matK sequences. Annals of the Missouri Botanical Garden 82: 149-175.
27. Kita, Y. and M. Ito. 2000. Nuclear ribosomal ITS sequences and phylogeny in East Asian Aconitum subgenus Aconitum (Ranunculaceae), with special reference to extensive polymorphism in individual plants. Plant Systematics and Evolution 225: 1-13.
28. Li, J., J. Ledger, T. Ward, and P. Del Tredici. 2004. Phylogenetics of Calycanthaceae based on molecular and morphological data, with a special reference to divergent paralogues of the nrDNA ITS region. Harvard Papers in Botany 9: 69-82.
29. Linder, C. R., L. R. Goertzen, B. V. Heuvel, J. Francisco-Ortega, and R. K. Jansen. 2000. The complete external transcribed spacer of 18S-26S rDNA: amplification and phylogenetic utility at low taxonomic levels in Asteraceae and closely allied families. Molecular Phylogenetics and Evolution 14: 285-303.
30. Markham, N. R. and M. Zuker. 2005. DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Research 33: W577-W581.
31. Mayol, M. and J. A. Rosselló. 2001. Why nuclear ribosomal DNA spacers (ITS) tell different stories in Quercus. Molecular Phylogenetics and Evolution 19: 167-176.
32. McDade, L. A. 1992. Hybrids and phylogenetic systematics II. The impact of hybrids on cladistic analysis. Evolution 46: 1329-1346.
33. Minin, V., Z. Abdo, P. Joyce, and J. Sullivan. 2003. Performance-based selection of likelihood models for phylogeny estimation. Systematic Biology 52: 1-10.
34. Muir, G., C. C. Fleming, and C. Schleotterer. 2001. Three divergent rDNA clusters predate the species divergence in Quercus petraea (Matt.) Liebl. and Quercus robur L. Molecular Biology and Evolution 18: 112-119.
35. Rambaut, A. 1996. Se-Al: Sequence Alignment Editor. Available at http://evolve.zoo.ox.ac.uk/.
36. Razafimandimbison, S. G., E. A. Kellogg, and B. Bremer. 2004. Recent origin and phylogenetic utility of divergent ITS putative pseudogenes: a case study from Naucleeae (Rubiaceae). Systematic Biology 53: 177-192.
37. Reznicek, A. A. 1990. Evolution in sedges (Carex, Cyperaceae). Canadian Journal of Botany 68: 1409-1432.
38. Roalson, E. H., J. T. Columbus, and E. A. Friar. 2001. Phylogenetic relationships in Cariceae (Cyperaceae) based on ITS (nrDNA) and trnT-L-F (cpDNA) region sequences: assessment of subgeneric and sectional relationships in Carex with emphasis on section Acrocystis. Systematic Botany 26: 318-341.
39. Ronquist, F. and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics (Oxford, England) 19: 1572-1574.
40. Ruggiero, M. V. and G. Procaccini. 2004. The rDNA ITS region in the Lessepsian marine angiosperm Halophila stipulacea (Forssk.) Aschers. (Hydrocharitaceae): Intragenomic variability and putative pseudogenic sequences. Journal of Molecular Evolution 58: 115-121.
41. Sanderson, M. T. and J. J. Doyle. 1992. Reconstruction of organismal and gene phylogenies from data on multigene families: concerted evolution, homoplasy and confidence. Systematic Biology 41: 4-17.
42. SantaLucia, J. 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proceedings of the National Academy of Sciences USA 95: 1460-1465.
43. Shimodaira, H. and M. Hasegawa. 1999. Multiple comparisons of log likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution 16: 1114-1116.
44. Small, R. L., R. C. Cronn, and J. F. Wendel. 2004. Use of nuclear genes for phylogeny reconstruction in plants. Australian Systematic Botany 17: 145-170.
45. Starr, J. R., R. J. Bayer, and B. A. Ford. 1999. The phylogenetic position of Carex section Phyllostachys and its implications for phylogeny and subgeneric circumscription in Carex (Cyperaceae). American Journal of Botany 86: 563-577.
46. Starr, J. R., S. A. Harris, and D. A. Simpson. 2003. Potential of the 5′ and 3′ ends of the intergenic spacer (IGS) of rDNA in the Cyperaceae: New sequences for lower level phylogenies in sedges with an example from Uncinia. International Journal of Plant Sciences 164: 213-227.
47. Starr, J. R., S. A. Harris, and D. A. Simpson. 2004. Phylogeny of the unispicate taxa in Cyperaceae tribe Cariceae I: Generic relationships and evolutionary scenarios. Systematic Botany 29: 528-544.
48. Swofford, D. L. 2001. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4.0 beta 10. Sunderland: Sinauer Associates.
49. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 24: 4876-4882.
50. Webber, J. M. and P. W. Ball. 1984. The taxonomy of the Carex rosea group in eastern Canada. Canadian Journal of Botany 62: 2058-2073.
51. Wei, X. X. and X. Q. Wang. 2004. Recolonization and radiation in Larix (Pinaceae): evidence from nuclear ribosomal DNA paralogues. Molecular Ecology 13: 3115-3123.
52. Wendel, J. F., A. Schnabel, and T. Seelanan. 1995a. An unusual ribosomal DNA sequence from Gossypium gossypioides reveals ancient, cryptic, intergenomic introgression. Molecular Phylogenetics and Evolution 4: 298-313.
53. Wendel, J. F., A. Schnabel, and T. Seelanan. 1995b. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proceedings of the National Academy of Sciences USA 92: 280-284.
54. Yang, Y. W., K. N. Lai, P. Y. Tai, D. P. Ma, and W. H. Li. 1999. Molecular phylogenetic studies of Brassica, Rorippa, Arabidopsis and allied genera based on the internal transcribed spacer region of 18S-25S rDNA. Molecular Phylogenetics and Evolution 13: 455-462.
55. Yen, A. C. and R. G. Olmstead. 2000. Molecular systematics of Cyperaceae tribe Cariceae based on two chloroplast DNA regions: ndhF and trnL intron-intergenic spacer. Systematic Botany 25: 479-494.
56. Zimmer, E. A., S. L. Martin, S. M. Beverley, Y. W. Kan, and A. C. Wilson. 1980. Rapid duplication and loss of genes coding for the alphachains of hemoglobin. Proceedings of the National Academy of Sciences USA 77: 2158-2162.