Phylogenetic relationships of diploid and polyploid species in Ludwigia sect. Isnardia (Onagraceae) based on chloroplast and nuclear DNAs

Taxon

Volumn 58, Issue 4, 2009, Pages 1216-1225

  Hung, Kuo Hsiang ^a   Schaal, Barbara A ^b   Hsu, Tsai Wen ^c   Chiang, Yu Chung ^a   Peng, Ching I ^d   Chiang, Tzen Yuh ^e  

^a NATIONAL PINGTUNG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Taiwan)

^b WASHINGTON UNIVERSITY   (United States)

^c ENDEMIC SPECIES RESEARCH INSTITUTE   (Taiwan)

^d BIODIVERSITY RESEARCH CENTER   (Taiwan)

^e NATIONAL CHENG KUNG UNIVERSITY   (Taiwan)

Author keywords

cpDNA atpB rbcL; Hybridization; Intergenic spacer; Ludwigia; Network; nrITS; Polyphyly; Polyploidy; sect. Isnardia

Indexed keywords

BIOMARKER; CHLOROPLAST; DICOTYLEDON; DIVERGENCE; DNA; GENEALOGY; HYBRIDIZATION; MAXIMUM LIKELIHOOD ANALYSIS; PHYLOGENY; RECONSTRUCTION; TYPE SPECIMEN;

LUDWIGIA; LUDWIGIA ARCUATA; LUDWIGIA BREVIPES; LUDWIGIA PALUSTRIS; LUDWIGIA REPENS; LUDWIGIA SPATHULATA; ONAGRACEAE;

EID: 71049127394     PISSN: 00400262     EISSN: None     Source Type: Journal    
DOI: 10.1002/tax.584013     Document Type: Article

References (72)

1. Andreas, M., Anand, P.T., Brian, W., Hongmei, J., Trevor, K., Rebecca, W.D., Robert, M. & Luca, C. 2005. Genomic changes in synthetic Arabidopsis polyploids. Pl. J. 41: 221-30.
2. Arnold, M.L. 1997. Natural Hybridization and Evolution. Oxford University Press, Oxford.
3. Baack, E.J. & Rieseberg, L.H. 2007. A genomic view of introgression and hybrid speciation. Curr. Opin. Genet. Developm. 17: 513-518.
4. Barton, N.H. 2001. The role of hybridization in evolution. Molec. Ecol. 10: 551-568.
5. Birky, C.W. 1995. Uniparental inheritance of mitochondrial and chloroplast genes mechanisms and evolution. Proc. Natl. Acad. Sci. U.S.A. 92: 11331-11338.
6. Buckler, E.S., Ippolito, A. & Holtsford, T.P. 1997. The evolution of ribosomal DNA: divergent paralogues and phylogenetic implications. Genetics 145: 821-832.
7. Chandler, G.T., Bayer, R.J. & Crisp, M.D. 2001. A molecular phylogeny of the endemic Australian genus Gastrolobium (Fabaceae: Mirbelieae) and allied genera using chloroplast and nuclear markers. Amer. J. Bot. 88: 1675- 1687.
8. Chiang, T.Y., Chiang, Y.C., Chen, Y.J., Chou, C.H., Havanond, S., Hong, T.N. & Huang, S. 2001. Phylogeogra-phy of Kandelia candel in East Asiatic mangroves based on nucleotide variation of chloroplast and mitochondrial DNAs. Molec. Ecol. 10: 2697-2710.
9. Chiang, Y.C., Hung, K.H., Schaal, B.A., Ge, X.J., Hsu, T.W. & Chiang, T.Y. 2006. Contrasting phylogeographical patterns between mainland and island taxa of the Pinus luchuensis complex. Molec. Ecol. 15: 765-779.
10. Chiang, T.Y., Schaal, B.A. & Peng, C.I. 1998. Universal primers of amplification and sequencing a noncoding spacer between atpB and rbcL genes of chloroplast DNA. Bot. Bull. Acad. Sin. 39: 245-250.
11. Coates, D.J. 1988. Genetic diversity and population genetic structure in the rare Chittering Grass Wattle, Acacia anomala Court. Austral. J. Bot. 36: 273-286.
12. Conti, E., Fischbach, A. & Sytsma, K.J. 1993. Tribal relationships in Onagraceae: implications from rbcL sequence data. Ann. Missouri Bot. Gard. 80: 672-685.
13. Conti, E., Soltis, D.E., Hardig, T.M. & Schneider, J. 1999. Phylogenetic relationships of the Silver Saxifrages (Saxifraga, sect. Ligulatae Haworth): implications for the evolution of substrate specificity, life histories, and biogeography. Molec. Phylog. Evol. 13: 536-555.
14. Cruzan, M.B. & Templeton, A.R. 2000. Paleoecology and coalescence: phylogeographic analysis of hypotheses from the fossil record. Trends Ecol. Evol. 15: 491-496.
15. Cui, L., Wall, P.K., Leebens-Mack, J.H., Lindsay, B.G., Soltis, D.E., Doyle, J.J., Soltis, P.S., Carlson, J.E., Arumuganathan, K., Barakat, A., Albert, V.A., Ma, H. & dePamphilis, C.W. 2006. Widespread genome duplications throughout the history of flowering plants. Genome Res. 16: 738-749.
16. De Bodt, S., Maere, S. & van de Peer, Y. 2005. Genome duplication and the origin of angiosperms. Trends Ecol. Evol. 20: 591-597.
17. Drummond, A.J., Ho, S.Y., Phillips, M.J. & Rambaut, A. 2006. Relaxed phylogenetics and dating with confidence. PLOS Biol. 4: e88.
18. Excoffier, L. & Smouse, P.E. 1994. Using allele frequencies and geographic subdivision to reconstruct gene trees within a species: molecular variance parsimony. Genetics 136: 343-359.
19. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
20. Felsenstein, J. 1993. Phylip (Phylogeny Inference Package), version 3.67. Department of Genetics, University of Washington. Available from http://evolution.genetics.washington.edu/phylip/phylip.html.
21. Ge, X.J., Chiang, Y.C., Chou, C.H. & Chiang, T.Y. 2005. Nested clade analysis of Dunnia sinensis (Rubiaceae), a monotypic genus from China based on organelle DNA sequences. Cons. Genet. 3: 251-362.
22. Grant, V. 1981. Plant Speciation, 2nd ed. Columbia University Press, New York.
23. Higgins, D.G., Bleasby, A.J. & Fuchs, R. 1992. CLUSTAL V: improved software for multiple sequence alignment. CABIOS 8: 189-191.
24. Huang, S., Chiang, Y.C., Schaal, B.A., Chou, C.H. & Chiang, T.Y. 2001. Organelle DNA phylogeography of Cycas taitungensis, a relict species in Taiwan. Molec. Ecol. 10: 2669-2681.
25. Jukes, T.H. & Cantor, C.R. 1969. Evolution of protein molecules. Pp. 31-132 in: Munroled, H.N. (ed.), Mammalian Protein Metabolism. Academic Press, New York.
26. Kim, Y.D. & Kim, S.H. 1999. Phylogeny of Weigela and Diervilla (Caprifoliaceae) based on nuclear rDNA internal transcribed spacer sequences. J. Pl. Res. 112: 331-341.
27. Kumar, S.K., Tamura, I.B. & Jakobsen, N.M. 2001. MEGA2: Molecular evolutionary genetics analysis software. Bio informatics 17: 1244-1245.
28. Lee, N.S., Sang, T., Crawford, D.J., Yeau, S.H. & Kim, S.C. 1996. Molecular divergence between disjunct taxa in eastern Asia and eastern North America. Amer. J. Bot. 83: 1373-78.
29. Levin, R.A., Wagner, W.L., Hoch, P.C., Nepokroeff, M., Pires, J.C., Zimmer, E.A. & Sytsma, K.J. 2003. Family-level relationships of Onagraceae based on chloroplast rbcL and ndhF data. Amer. J. Bot. 90: 107-115.
30. Liu, B., Brubaker, C.L., Mergeai, G., Cronn, R.C. & Wendel, J.F. 2001. Polyploid formation in cotton is not accompanied by rapid genomic changes. Genome 44: 321-330.
31. Maguire, T.L. & Sedgley, M. 1997. Genetic diversity in Banksia and Dryandra (Proteaceae) with emphasis on Banksia cuneata, a rare and endangered species. Heredity 79: 394-401.
32. McClintock, B. 1984. The significance of responses of the genome to challenge. Science 226: 792-801.
33. Murray, M.G. & Thompson, W.F. 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 8: 4321-4325.
34. Ohi, T., Kajita, T. & Murata, J. 2003. Distinct geographic structure as evidenced by chloroplast DNA haplotypes and ploidy level in Japanese Aucuba (Aucubaceae). Amer. J. Bot. 90: 1645-1652.
35. Ohsako, T. & Ohnishi, O. 2000. Intra- and interspecific phylogeny of wild Fagopyrum (Polygonaceae) species based on nucleotide sequences of noncoding region in chloroplast DNA. Amer. J. Bot. 87: 573-582.
36. O'Kane, S.L. 1993. Molecular Systematics of Lopezia (Onagraceae). Ph.D. Dissertation, Division of Biology and Biomedical Sciecnes, Washington University, St. Louis.
37. Orive, M.E. & Asmussen, M.A. 2000. The effects of pollen and seed migration on nuclear-dicytoplasmic systems. II. A new method for estimating plant gene flow using joint nuclear-cytoplasmic data. Genetics 155: 833-854.
38. Ozkan, H., Levy, A.A. & Feldman, M. 2001. Allopolyploidy induced rapid genome evolution in the wheat (Aegilops-Triticum) group. Pl. Cell 13: 1735-1747.
39. Peng, C.I, Schmidt, C.L., Hoch, P.C. & Raven, P.H. 2005. Systematics and evolution of Ludwigia sect. Dantia (Onagraceae). Ann. Missouri Bot. Gard. 92: 307-359.
40. Ramakrishnanelizabeth, U., Hadlyjoanna, A. & Mountain, L. 2005. Detecting past population bottlenecks using temporal genetic data. Molec. Ecol. 14: 2915-2924.
41. Ramamoorthy, T.P. & Zardini, E.M. 1987. The systematics and evolution of Ludwigia sect. Myrtocarpus s. lat.(Onagraceae). Monogr. Syst. Bot. Missouri Bot. Gard. 19: 1-120.
42. Rambaut, A. & Drummond, A. 2004. Tracer - MCMC trace analysis tool. University of Oxford, Oxford.
43. Ramsey, J. & Schemske, D.W. 1998. Pathways, mechanisms, and rates of polyploid formation in flowering plants. Annual Rev. Ecol. Syst. 29: 467-501.
44. Raven, P.H. 1963. The Old World species of Ludwigia (including Jussiaea), with a synopsis of the genus (Onagraceae). Reinwardtia 6: 327-427.
45. Raven, P.H. 1988. Onagraceae as a model of plant evolution. Pp. 85-107 in: Gottlieb, L. & Jain, S. (eds.), Plant Evolutionary Biology. Chapman and Hall, London.
46. Raven, P.H. & Tai, W. 1979. Observations of chromosomes in Ludwigia (Onagraceae). Ann. Missouri Bot. Gard. 66: 862-879.
47. Rieseberg, L.H. 1998. Genetic mapping as a tool for studying speciation. Pp. 459-487 in: Soltis, D.E., Soltis, P.S. & Doyle, J.J. (eds.), Molecular Systematics of Plants II: DNA Sequencing. Kluwer, Norwell.
48. Rieseberg, L.H. & Carney, S.E. 1998. Tansley Review no. 102. Plant hybridization. New Phytol. 140: 599-624.
49. Rossetto, M.P., Weaver, K. & Dixon, K.W. 1995. Use of RAPD analysis in devising conservation strategies for the rare and endangered Grevillea scapigera (Proteaceae). Molec. Ecol. 4: 357-364.
50. Rozas, J. & Rozas, R. 1999. DnaSP version 3.0: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15: 174-175.
51. Schnabel, A. & Wendel, J.F. 1998. Cladistic biogeography of Gleditsia (Legumino sae) based on ndhF and rpl16 chloroplast gene sequences. Amer. J. Bot. 85: 1753-1765.
52. Shaked, H., Kashkush, K., Ozkan, H., Feldman, M. & Levy, A.A. 2001. Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Pl. Cell 13: 1749-1759.
53. Slotte, T., Ceplitis, A., Neuffer, B., Hurka, H. & Lascoux, M. 2006. Intrageneric phylogeny of Capsella (Brassicaceae) and the origin of the tetraploid C. bursa-pastoris based on chloroplast and nuclear DNA sequences. Amer. J. Bot. 93: 1714-1724.
54. Smedmark, J.E.E., Eriksson, T., Evans, R.C. & Campbell, C.S. 2003. An allopolyploid speciation in Geinae (Rosaceae): evidence from nucelar granule-bound starch synthase (GBSSI) gene sequences. Syst. Biol. 52: 374-385.
55. Soltis, D.E., Bell, C.D., Kim, S. & Soltis, P.S. 2008. Origin and early evolution of angiosperms. Ann. New York Acad. Sci. 1133: 3-25.
56. Soltis, D.E. & Kuzo, R.K. 1995. Discordance between nuclear Hung & al.and chloroplast phylogenies in the Heuchera group (Saxifragaceae). Evolution 49: 727-742.
57. Soltis, D.E. & Soltis, P.S. 1999. Polyploidy: recurrent formation and genome evolution. Trends Ecol. Evol. 14: 348-352.
58. Soltis, D.E., Soltis, P.S. & Tate, J.A. 2003. Advances in the study of polyploidy since Plant Speciation. New Phytol. 161: 173-191.
59. Soltis, P.S., Plunkett, G.M., Novak, S.J. & Soltis, D.E. 1995. Genetic variation in Tragopogon species: additional origins of the allotetraploids T. mirus and T. miscellus (Compositae). Amer. J. Bot. 82: 1329-1341.
60. Song, B.H., Wang, X.Q., Wang, X.R., Sun, L.J., Hong, D.Y. & Peng, P.H. 2002. Maternal lineages of Pinus densata, a diploid hybrid. Molec. Ecol. 11: 1057-1063.
61. Stebbins, G.L. 1950. Variation and Evolution in Plants. Columbia University Press, New York.
62. Stebbins, G.L. 1971. Chromosomal Evolution in Higher Plants. Edward Arnold, London.
63. Stebbins, G.L. 1980. Polyploidy in plants: unsolved problems and prospects. Pp. 495-520 in: Lewis, W.H. (ed.), Polyploidy: Biological Relevance. Plenum Press, New York.
64. Sytsma, K.J., Smith, J.F. & Hoch, P.C. 1991. A chloroplast DNA analysis of tribal and generic relationships with Onagraceae. Amer. J. Bot. 78: 222. [Abstract]
65. Turelli, M., Barton, N.H. & Coyne, J.A. 2001. Theory and speciation. Trends Ecol. Evol. 16: 330-343.
66. Wen, J., Jansen, R.K. & Kilgore, K. 1996. Evolution of the eastern Asian and eastern North American disjunct genus Symplocarpus (Araceae): insights from chloro plast DNA restriction site data. Biochem. Syst. Ecol. 24: 735-747.
67. Wendel, J.F. 2000. Genome evolution in polyploids. Pl. Molec. Biol. 42: 225-249.
68. White, T.J., Bruns, T., Lee, S. & Taylor, J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Pp. 315-322 in: Michael, A.I., David, H.G., John, J.S. & Thomas, J.W. (eds.), PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego.
69. Wilson, C.A. 2003. Phylogenetic relationships in Iris series Californicae based on ITS sequences of nuclear ribosomal DNA. Syst. Bot. 28: 39-46.
70. Veitia, R.A. 2005. Paralogs in polyploids: one for all and all for one? Pl. Cell 17: 4-11.
71. Zardini, E.M. & Raven, P.H. 1992. A new section of Ludwigia (Onagraceae) with a key to the sections of the genus. Syst. Bot. 17: 481-485.
72. Zawko, G., Krauss, S.L., Dixon, K.W. & Sivasithamparam, K. 2001. Conservation genetics of the rare and endangered Leucopogon obtectus (Ericaceae). Molec. Ecol. 10: 2389-2396.