Comprehensive molecular phylogeny of the sub-family dipterocarpoideae (Dipterocarpaceae) based on chloroplast DNA sequences

Genes and Genetic Systems

Volumn 81, Issue 1, 2006, Pages 1-12

  Gamage, Dayananda Thawalama ^a   De Silva, Morley P ^b   Inomata, Nobuyuki ^a   Yamazaki, Tsuneyuki ^c   Szmidt, Alfred E ^a  

^a KYUSHU UNIVERSITY   (Japan)

^b UNIVERSITY OF RUHUNA   (Sri Lanka)

^c Research Institute of Evolutionary Biology   (Japan)

Author keywords

Chloroplast DNA; Dipterocarpoideae; Doona; Molecular phylogeny; Monotes

Indexed keywords

CHLOROPLAST DNA;

ARTICLE; DIPTEROCARPOIDEAE; DNA SEQUENCE; GENE SEQUENCE; MADAGASCAR; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT; PLANT GENETICS; SEYCHELLES; SRI LANKA; TAXONOMY; TILIACEAE; TREE; UNINDEXED SEQUENCE;

CHLOROPLASTS; DNA, CHLOROPLAST; PHYLOGENY; SEQUENCE ANALYSIS, DNA; THEALES;

DIPTEROCARPACEAE; DOONA; HOPEA; MALVACEAE; MONOTES; SHOREA; STEMONOPORUS; VATERIA;

EID: 33645826284     PISSN: 13417568     EISSN: 13417568     Source Type: Journal    
DOI: 10.1266/ggs.81.1     Document Type: Article

References (48)

1. Ashton, P. S., (1972) Precursor to a taxonomic revision of Ceylon Dipterocarpaceae. Blumea 20, 357-366.
2. Ashton, P. S., (1977) Dipterocarpaceae. Revised handbook flora of Ceylon. 2, 166-196.
3. Ashton, P. S., (1979) Phylogenetic speculations on Dipterocarpaceae. Histoire Natur. Paris N. S. (B) 26, 145-149.
4. Ashton, P. S., (1980) Dipterocarpaceae. In: Revised Handbook to the Flora of Ceylon I (eds.: M. D. Dassanayake, and F. R. Fosberg), pp. 364-423. New Delhi.
5. Ashton, P. S., (1982) Dipterocarpaceae. Flora Malesiana 9, 237-552.
6. Ashton, P. S., and Gunatilleke, C. V. S., (1987) New light on the plant geography of Ceylon. I Historical plant geography, J. Biogeog. 14, 249-285.
7. Bossuyt, F., Meegaskumbura, M., Beenaerts, N., Gower, D. J., Pethiyagoda, R., Roelants, K., Mannaert, A., Wilkinson, M., Bahir, M. M., Arachchi, K. M., Ng, P. K. L., Schneider, C. J., Oommen, O. V., and Milinkovitch, M. C., (2004) Local Endemism Within the Western Ghats-Sri Lanka Biodiversity Hotspot. Science 306, 479-480.
8. Brandis, D., (1895) An enumeration of the Dipterocarpaceae. J. Linnean Soc. 31, 1-148.
9. Chiu, W. L., and Sears, B. B., (1985) Recombination between chloroplast DNAs does not occur in sexual crosses of Oenothera. Mol. Gen. Genet. 198, 525-528.
10. Dayanandan, S., Ashton, P. S., M., W., and Primack, R. B., (1999) Phylogeny of the tropical tree family Dipterocarpaceae based on nucleotide sequences of the chloroplast rbcL gene. Am. J. Bot. 86, 1182-1190.
11. Felsenstein, J., (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17, 368-376.
12. Felsenstein, J., (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
13. Felsenstein, J., (2004) PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Science, University of Washington, Seattle.
14. Gamage, D. T., de Silva, M., Yoshida, A., Szmidt, A. E., and Yamazaki, T., (2003) Molecular phylogeny of Sri Lankan Dipterocarpaceae in relation to other Asian Dipterocarpaceae based on chloroplast DNA sequences. Tropics 13, 79-87.
15. Gilg, E., (1925) Dipterocarpaceae in Engler und Prantl. Natürliche Pflanzenfamilien 21, 237-269.
16. Gotwald, H., and Parameswaran, N., (1966) Das sekundäre Xylem der Familie Dipterocarpaceae, Anatomische Untersuchungen zur Taxonomie und Phylogenie. Bot. Jahrb. Syst. 85, 410-508.
17. Hall, T. A., (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids. Symp. 41, 95-98.
18. Heim, F., (1892) Recherches sur les Diptérocarpacées. Ph. D. dissertation, à la Faculte des Sciences de Paris. pp. 1-186.
19. Jong, K., and Kaur, A., (1979) A cytotaxonomic view of Dipterocarpaceae with some comments on polyploidy and apomixis. In: Diptérocarpacé es: Taxonomie-Phylogénie-Ecologie (ed.: G. Maury-Lechon), pp. 41-49. Mémoires du Muséum National d 'Histoire Naturelle: Série B, Botanique, Editions du Muséum, Paris.
20. Jong, K., and Lethbridge, A., (1967) Cytological studies in the Dipterocarpaceae. I. Chromosome numbers of certain Malaysian genera. Notes from the Royal Garden Edinburgh 27, 175-184.
21. Kajita, T., Kamiya, K., Nakamura, K., Tachida, H., Wickneswari, R., Tsumura, Y., Yoshimaru, H., and Yamazaki, T., (1998) Molecular Phylogeny of Dipterocarpaceae in Southeast Asia Based on Nucleotide Sequences of matK, trnL intron and trnL-trnF Intergenic Spacer Region in Chloroplast DNA. Mol. Phyl. Evol. 10, 202-209.
22. Kamiya, K., Harada, K., Ogino, K., Kajita, T., Yamazaki, T., Lee, H. S., and Ashton, P. S., (1998) Molecular Phylogeny of Dipterocarp Species Using Nucleotide Sequences of Two Non-coding Regions in Chloroplast DNA. Tropics 7, 195-207.
23. Kamiya, K., Harada, K., Tachida, H., and Ashton, P. S., (2005) Phylogeny of PgiC gene in Shorea and its closely related genera (Dipterocarpaceae), the dominant trees in Southeast Asian tropical rain forests. Am. J. Bot. 92, 775-788.
24. Kimura, M., (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111-120.
25. Kostermans, A. J. G. H., (1978) Pakaraimaea Dipterocarpaceae Maguire and Ashton belongs to Tiliaceae and not to Dipterocarpaceae. Taxon 27, 357-359.
26. Kostermans, A. J. G. H., (1982) The genus Hopea (Dipterocarpaceae) in Ceylon, Sri Lanka. Ceylon J. Biol. Sci. 15, 41-49.
27. Kostermans, A. J. G. H., (1984) Monograph of the genus Doona Thw. (Dipterocarpaceae). Botanische Jahrbücher. Systematik Pflazengeschichte und Pflanzengeographie 104, 425-454.
28. Kostermans, A. J. G. H., (1985) Family status of the Monotoideae Gilg. and the Pakaraimoideae Ashton, Maguire and de Zeeuw (Dipterocarpaceae). Taxon 34, 426-435.
29. Kostermans, A. J. G. H., (1989) Monotaceae, a new family allied to Tiliaceae. Taxon 38, 123-124.
30. Kostermans, A. J. G. H., (1992) A handbook of the Dipterocarpaceae of Sri Lanka. The Wildlife Heritage Trust of Sri Lanka, Colombo, Sri Lanka, pp. 243.
31. Maury, G., (1978) Dipterocarpacees: du fruit a la plantule. Ph. D. thesis. Université Paul Sabatier, Toulouse, Paris. pp. 3 vols., IA: 243p.,
32. Maury, G., Dipterocarpacees: du fruit a la plantule. IB: 432p.,
33. Maury, G., Dipterocarpacees: du fruit a la plantule. II: 344p.
34. Maury-Lechon, G., (1979) Conséquences taxonomiques de l'étude des caractères des fruits/ germinations, embryons et plantules des Diptérocarpacées. In: Diptérocarpacé es: Taxonomie-Phylogénie-Ecologie (ed.: G. Maury-Lechon), pp. 81-106. Mémoires du Muséum National d'Histoire Naturelle: First International Round Table on Dipterocarpaceae, Série B, Botanique 26, Editions du Muséum, Paris.
35. Maury-Lechon, G., and Curtet, L., (1998) Biogeography and Evolutionary Systematics of Dipterocarpaceae. In: A Review of Dipterocarps: Taxonomy, Ecology and Silviculture (eds.: S. Appanah, and J. M. Turnbull), pp. 5-44. Center for International Forest Research, Bogor, Indonesia.
36. Meijer, W., (1979) Taxonomic studies in the genus Dipterocarpus. In: Diptérocarpacées: Taxonomie-Phylogénie-Ecologie (ed.: G. Maury-Lechon), pp. 50-56. Mémoires du Muséum National d'Histoire Naturelle: Série B, Botanique 26, Editions du Muséum, Paris.
37. Meijer, W., and Wood, G. H. S., (1964) Dipterocarps of Sabah (North Borneo). Sabah forest record No. 5, Forest Department, Sandakan, Art Printing Works, Kuala Lumpur, Malaysia, pp. 1-344.
38. Meijer, W., and Wood, G. H. S., (1976) Keys to Dipterocarps on Sabah. Biotrop, Bogor, Indonesia.
39. Morton, C. M., Dayanandan, S., and Dissanayake, D., (1999) Phylogeny and biosystematics of Pseudomonotes (Dipeterocarpaceae) based on molecular and morphological data. Pl. Syst. Evol. 216, 197-205.
40. Lys(UUU) gene from mustard (Sinapis alba) contains a class II intron potentially coding for a maturase-related polypeptide. Curr. Gene. 11, 251-257.
41. Oginuma, K., Kono, Y., and Tobe, H., (1999) Embryology of Vateriopsis (Dipterocarpaceae) and relationships of the family. In: Abstract for the XVI International Botanical Congress, http://www.biologie.uni-hamburg.de/bonline/ ibc99/ibc/abstracts/listen/abstracts/3183.html.
42. Ooi, K., Endo, Y., Yokoyama, J., and Murakami, N., (1995) Useful primer designs to amplify DNA fragments of the plastid gene matK from Angiosperm plants. J. Jap. Bot. 70, 328-331.
43. Parameswaran, N., and Gotwald, H., (1979) Problematic taxa in the Dipterocarpaceae. Their Anatomy and Taxonomy. In: Dipterocarpacees: Taxonomie-Phylogénie-Ecologie (ed.: G. Maury-Lechon), pp. 69-75. Mémoires du Muséum National d'Histoire Naturelle: First International Round Table on Dipterocarpaceae, Editions du Muséum, Paris.
44. Saitou, N., and Nei, M., (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
45. Symington, C. F., (1943) Foresters, manual of Dipterocarps. Malayan forest records No. 16, Penerbit Universiti Malaya, Kuala Lumpur, Malaysia, pp. 244.
46. Taberlet, P., Gielly, L., Pautou, G., and Bouvet, J., (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Pl. Mol. Biol. 17, 1105-1109.
47. Thompson, J. D., Gibson, T. J., Plewniak, F., and Higgins, D. G., (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24, 4876-4882.
48. Tsumura, Y., Kawahara, T., Wickneswari, R., and Yoshimura, K., (1996) Molecular phylogeny of Dipterocarpaceae in Southeast Asia using RFLP of PCR-amplified chloroplast genes. Theor. Appl. Genet. 93, 22-29.