A non-coding plastid DNA phylogeny of Asian Begonia (Begoniaceae): Evidence for morphological homoplasy and sectional polyphyly

Molecular Phylogenetics and Evolution

Volumn 60, Issue 3, 2011, Pages 428-444

  Thomas, D C ^a,b   Hughes, M ^a   Phutthai, T ^c   Rajbhandary, S ^d   Rubite, R ^e   Ardi, W H ^f   Richardson, J E ^a  

^a ROYAL BOTANIC GARDEN EDINBURGH   (United Kingdom)

^b UNIVERSITY OF HONG KONG   (Hong Kong)

^c PRINCE OF SONGKLA UNIVERSITY   (Thailand)

^d TRIBHUVAN UNIVERSITY   (Nepal)

^e UNIVERSITY OF THE PHILIPPINES MANILA   (Philippines)

^f Bogor Botanic Gardens   (Indonesia)

Author keywords

Asia; Begonia; Begoniaceae; Character evolution; Phylogeny

Indexed keywords

CHLOROPLAST DNA; PLANT DNA; RIBOSOMAL SPACER DNA;

ARTICLE; BAYES THEOREM; BEGONIACEAE; CLASSIFICATION; DNA SEQUENCE; FRUIT; GENETICS; OVULE; PHYLOGENY; STATISTICAL MODEL;

BAYES THEOREM; BEGONIACEAE; DNA, CHLOROPLAST; DNA, PLANT; DNA, RIBOSOMAL SPACER; FRUIT; LIKELIHOOD FUNCTIONS; OVULE; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

BEGONIA; BEGONIACEAE; PETERMANNIA; PLATYCENTRUM;

EID: 79959661805     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2011.05.006     Document Type: Article

References (81)

1. Badcock, Z., 1998. A phylogenetic investigation of Begonia L. section Knesebeckia (Klotzsch) A.D.C. PhD thesis. University of Glasgow, Glasgow.
2. Borsch T., Quandt D. Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA. Plant Syst. Evol. 2009, 282:169-199.
3. Burnham K.P., Anderson D.R. Multimodel inference: understanding AIC and BIC in model selection. Sociol. Method Res. 2004, 33:261-304.
4. Chiang T.Y., Hong K.H., Peng C.I. Experimental hybridization reveals biased inheritance of the internal transcribed spacer of the nuclear ribosomal DNA in Begonia x taipieiensis. J. Plant Res. 2001, 114:343-351.
5. Clarke C.B. Begoniaceae. Flora of British India 1879, 635-656. L. Reeve & Co., London. J.D. Hooker (Ed.).
6. De Candolle A. Begoniaceae. Prodromus Systematis Naturalis Regni Vegetabilis 1864, 266-408. Masson and Sons, Paris. A. De Candolle (Ed.).
7. Doorenbos J., Sosef M.S.M., de Wilde J.J.F.E. The Sections of Begonia: Including Descriptions, Keys and Species Lists 1998, Agricultural University, Wageningen.
8. Drummond, A.J., Ashton, B., Buxton, S., Cheung, M., Cooper, A., Heled, J., Kearse, M., Moir, R., Stones-Havas, S., Sturrock, S., Thierer, T., Wilson, A., 2010. Geneious v5.1. http://www.geneious.com/.
9. Edgar R.C. MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004, 5:113.
10. Fazekas A.J., Steeves R., Newmaster S.G. Improving sequencing quality from PCR products containing long mononucleotide repeats. Biotechniques 2010, 48:277-285.
11. Forrest, L.L., 2001. Phylogeny of Begoniaceae. PhD thesis. University of Glasgow, Glasgow.
12. Forrest L.L., Hollingsworth P.M. A recircumscription of Begonia based on nuclear ribosomal sequences. Plant Syst. Evol. 2003, 241:193-211.
13. Forrest L.L., Hughes M., Hollingsworth P.M. A phylogeny of Begonia using nuclear ribosomal sequence data and morphological characters. Syst. Bot. 2005, 30:671-682.
14. Frodin D.G. History and concepts of big plant genera. Taxon 2004, 53:753-776.
15. Goodall-Copestake W.P., Perez-Espona S., Harris D.J., Hollingsworth P.M. The early evolution of the mega-diverse genus Begonia (Begoniaceae) inferred from organelle DNA phylogenies. Biol. J. Linn. Soc. 2010, 101:243-250.
16. Graham S.W., Reeves P.A., Burns A.C.E., Olmstead R.G. Microstructural changes in noncoding chloroplast DNA: interpretation, evolution, and utility of indels and inversions in basal angiosperm phylogenetic inference. Int. J. Plant Sci. 2000, 161:S83-S96.
17. Gu C.Z. Infrageneric classification of Begonia. Flora of China 2007, 205-207. Science Press, Beijing. Z.Y. Wu, P.H. Raven, D.Y. Hong (Eds.).
18. Gu C.Z., Peng C.I., Turland N.J. Begoniaceae. Flora of China 2007, 153-207. Science Press, Beijing. Z.Y. Wu, P.H. Raven, D.Y. Hong (Eds.).
19. Huelsenbeck J.P., Rannala B. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst. Biol. 2004, 53:904-913.
20. Huelsenbeck J.P., Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17:754-755.
21. Hughes M. An Annotated Checklist of Southeast Asian Begonia 2008, Royal Botanic Garden Edinburgh, Edinburgh, U.K.
22. Hughes, M., Pullan, M., 2007. Southeast Asian Begonia database. http://elmer.rbge.org.uk/begonia/.
23. Hughes M., Coyle C., Rubite R.R. A revision of Begonia section Diploclinium (Begoniceae) on the Philippine island of Palawan, including five new species. Edinburgh J. Bot. 2010, 67:123-140.
24. Hughes M., Girmansyah D., Ardi W.H., Nurainas Seven new species of Begonia from Sumatra. Gard. Bull. Singapore 2009, 61:29-44.
25. Irmscher E. Die Verteilung der Geschlechter in den Inflorescenzen der Begoniaceen unter Berücksichtigung der morphologischen Verhältnisse. Bot. Jahrb. Syst. 1914, 50:556-577.
26. Irmscher E. Begoniaceae. Naturlichen Pflanzenfamilien 1925, 548-588. Wilhelm Engelmann, Leipzig. A. Engler, K. Prantl (Eds.).
27. Irmscher E. Die Begoniaceen der Malaiischen Halbinsel. Mitt. Inst. Allg. Bot. Hamburg 1929, 8:86-160.
28. Irmscher E. Die Begonien Chinas und ihre Bedeutung für die Frage der Formbildung in polymorphen Sippen. Mitt. Inst. Allg. Bot. Hamburg 1939, 10:431-557.
29. Jayasuriya A.H.M. Begoniaceae. Flora of Ceylon 1983, 137-152. Amerind Publishing, New Delhi. M.D. Dassanayake, F.R. Fosberg (Eds.).
30. Kass R.E., Raftery A.E. Bayes factors. J. Am. Stat. Assoc. 1995, 90:773-795.
31. Kelchner S.A. The evolution of non-coding chloroplast DNA and its application in plant systematics. Ann. Missouri Bot. Gard. 2000, 87:482-498.
32. Kidner C.A., Umbreen S. Why is leaf shape so variable?. Int. J. Dev. Biol. 2010, 4:64-75.
33. Kiew R. The limestone Begonias of Sabah, Borneo: flagship species for conservation. Gard. Bull. Singapore 2001, 53:241-286.
34. Kiew, R., 2005. Begonias of Peninsular Malaysia. Natural History Publications (Borneo), Kota Kinabalu.
35. Kiew R., Sang J. Seven new species of Begonia (Begoniaceae) from the Ulu Merirai and Bukit Sarang limestone areas in Sarawak, Borneo. Gard. Bull. Singapore 2009, 60:351-372.
36. Kiew R., Teo L.L., Gan Y.Y. Assessment of the hybrid status of some Malesian plants using Amplified Fragment Length Polymorphism. Telopea 2003, 10:225-233.
37. Klotzsch J.F. Begoniaceen: Gattungen und Arten 1854, Abhandlungen der Königlichen Akademie der Wissenschaften zu Berlin, Berlin.
38. Ku, S.M., 2006. Systematics of Begonia sect. Coelocentrum (Begoniaceae) of China. MSc thesis. National Cheng-Kung University, Tainan.
39. Ku T.C. Begoniaceae. Flora Reipublicae Popularis Sinica 1999, Science, Press, Beijing, pp. 126-269, 401-402. T.C. Ku (Ed.).
40. Legro R.A.H., Doorenbos J. Chromosome numbers in Begonia. Netherlands J. Agric. Sci. 1969, 17:189-202.
41. Legro R.A.H., Doorenbos J. Chromosome numbers in Begonia 2. Netherlands J. Agric. Sci. 1971, 19:176-183.
42. Legro R.A.H., Doorenbos J. Chromosome numbers in Begonia 3. Netherlands J. Agric. Sci. 1973, 21:167-170.
43. Lewis P.O. A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 2001, 50:913-925.
44. Löhne C., Borsch T. Molecular evolution and phylogenetic utility of the petD group II intron: a case study in basal angiosperms. Mol. Biol. Evol. 2005, 22:317-332.
45. Maddison, W.P., Maddison, D.R., 2010. Mesquite: A Modular System for Evolutionary Analysis. Version 2.7.4.
46. Matolweni L.O., Balkwill K., McLellan T. Genetic diversity and gene flow in the morphologically variable, rare endemics Begonia dregei and Begonia homonyma (Begoniaceae). Am. J. Bot. 2000, 87:431-439.
47. Neale S., Goodall-Copestake W., Kidner C. The evolution of diversity in Begonia. Floriculture, Ornamental and Plant Biotechnology: Advances and Topical Issues 2006, 606-611. Global Science Books, Isleworth, UK. J.A. Teixeira da Silva (Ed.).
48. Newton M.A., Raftery A.E. Approximate Bayesian inference with the weighted likelihood bootstrap. J. Roy. Stat. Soc. B Met. 1994, 56:3-48.
49. Nylander J.A.A., Wilgenbusch J.C., Warren D.L., Swofford D.L. AWTY (Are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 2008, 24:581-583.
50. Oginuma K., Peng C.I. Karyomorphology of Taiwanese Begonia (Begoniaceae): Taxonomic implications. J. Plant Res. 2002, 115:225-235.
51. Peng C.I., Chen Y.K. Hybridity and parentage of Begonia buimontana Yamamoto (Begoniaceae) from Taiwan. Ann. Missouri Bot. Gard. 1991, 78:995-1001.
52. Peng C.I., Chiang T.Y. Molecular confirmation of unidirectional hybridization in Begonia x taipeiensis Peng (Begoniaceae) from Taiwan. Ann. Missouri Bot. Gard. 2000, 87:273-285.
53. Peng C.I., Ku S.M. Begonia x chungii (Begoniaceae), a new natural hybrid in Taiwan. Bot. Stud. (Taipei) 2009, 50:241-250.
54. Peng C.I., Sue C.Y. Begonia x taipeiensis (Begoniaceae), a new natural hybrid in Taiwan. Bot. Bull. Acad. Sin. 2000, 41:151-158.
55. Phutthai T., Sands M., Sridith K. Field surveys of natural populations of Begonia L. in Thailand. Thai Forest Bull. Bot. 2009, 186-196. (special issue).
56. Plana V., Gascoigne A., Forrest L.L., Harris D., Pennington R.T. Pleistocene and pre-Pleistocene Begonia speciation in Africa. Mol. Phylogen. Evol. 2004, 31:449-461.
57. Posada D. JModelTest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 25:1253-1256.
58. Posada D., Buckley T.R. Model selection and model averaging in phylogenetics: advantages of akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 2004, 53:793-808.
59. Rajbhandary, S., 2010. Systematic revision of the genus Begonia L. (Begoniaceae) in the Himalayas. PhD thesis. Tribhuvan University, Kathmandu, Nepal.
60. Rambaut, A., Drummond, A.J., 2009. Tracer v1.5. http://beast.bio.ed.ac.uk/Tracer.
61. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
62. Rubite, R.R., 2010. Systematic studies on Philippine Begonia L. secion Diploclinium (Lindl.) A. D.C. (Begoniaceae). PhD thesis. De La Salle University, Manila.
63. Sands M.J.S. The Begonias of New Guinea - an overview. Blumea 2009, 54:272-277.
64. Shaw J., Lickey E.B., Schilling E.E., Small R.L. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am. J. Bot. 2007, 94:275-288.
65. Shinde D., Lai Y.L., Sun F.Z., Arnheim N. Taq DNA polymerase slippage mutation rates measured by PCR and quasi-likelihood analysis: (CA/GT)(n) and (A/T)(n) microsatellites. Nucleic Acids Res. 2003, 31:974-980.
66. Shui Y.M., Peng C.I., Wu C.Y. Synopsis of the Chinese species of Begonia (Begoniaceae), with a reappraisal of sectional delimitation. Bot. Bull. Acad. Sin. 2002, 43:313-327.
67. Shui Y.-M., Chen W.-H. Revision to sect. Petermannia of Begonia (Begoniaceae) in China. Acta Bot. Yunnan. 2004, 26:482-486.
68. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
69. Suchard M.A., Weiss R.E., Sinsheimer J.S. Bayesian selection of continuous-time Markov chain evolutionary models. Mol. Biol. Evol. 2001, 18:1001-1013.
70. Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequences. Some Mathematical Questions in Biology - DNA Sequence Analysis 1986, 57-86. American Mathematical Society, Providence, RI. R.M. Miura (Ed.).
71. Tebbitt M.C. Taxonomy of Begonia longifolia Blume (Begoniaceae) and related species. Brittonia 2003, 55:19-29.
72. Tebbitt M.C. Begonias: Cultivation, Identification, and Natural History 2005, Timber Press, Portland, Or.
73. Tebbitt M.C., Dickson J.H. Amended descriptions and revised sectional assignment of some Asian Begonias (Begoniaceae). Brittonia 2000, 52:112-117.
74. Tebbitt M.C., Lowe-Forrest L., Santoriello A., Clement W.L., Swensen S.M. Phylogenetic relationships of Asian Begonia, with an emphasis on the evolution of rain-ballist and animal dispersal mechanisms in sections Platycentrum, Sphenanthera and Leprosae. Syst. Bot. 2006, 31:327-336.
75. Tebbitt M.C., MacIver C.M. The systematic significance of the endothecium in Begoniaceae. Bot. J. Linn. Soc. 1999, 131:203-221.
76. Teo L.-L., Kiew R. First record of a natural Begonia hybrid in Malaysia. Gard. Bull. Singapore 1999, 51:103-118.
77. Thomas, D.C., 2010. Phylogenetics and historical biogeography of Southeast Asian Begonia L. (Begoniaceae). PhD thesis. University of Glasgow, Glasgow.
78. Thomas D.C., Ardi W.H., Hughes M. Two new species of Begonia (Begoniaceae) from Central Sulawesi, Indonesia. Edinburgh J. Bot. 2009, 66:103-114.
79. Thomas D.C., Ardi W.H., Hughes M. Nine new species of Begonia (Begoniaceae) from South and West Sulawesi, Indonesia. Edinburgh J. Bot. 2011, 68:1-31.
80. Uddin A. Distribution and status of Indian Begonia L. species. J. Econ. Taxon. Bot. 2007, 31:591-597.
81. Warburg O. Begoniaceae. Naturlichen Pflanzenfamilien 1894, 121-150. Wilhelm Engelmann, Leipzig. A. Engler, K. Prantl (Eds.).