Abstract
In order to construct a molecular phylogeny of Indonesian Dipterocarpoideae (Dipterocarpaceae), PCR-RFLP of the chloroplast regions rbcL, petB, psbA, psaA, and trnL-F was performed with seven restriction enzymes in 129 samples including 58 species from nine genera. In the strict consensus tree with Monotes kerstingii as outgroup Indonesian Dipterocarpaceae were divided into two major clades. One clade (bootstrap value=71) consisted of Upuna, Cotylelobium, Anisoptera, Vatica, Dipterocarpus (tribe Dipterocarpeae, bootstrap value=83) and Dryobalanops (tribe Shoreae, bootstrap value=99) in a basal position. The second clade consisted of Hopea, Parashorea, and Shorea (tribe Shoreae) with 95% bootstrap support. Tribe Dipterocarpeae is monophyletic, tribe Shoreae is polyphyletic since Dryobalanops is sister to tribe Dipterocarpeae. In the neighbour-joining tree the sister group position of Dryobalanops to tribe Dipterocarpeae is not supported by the bootstrap analysis. Alternatively, we used Upuna borneensis as outgroup. The effect of outgroup selection on tree topology, taxonomic classification and the interpretation of character evolution is discussed.
Similar content being viewed by others
References
W. S. Alverson K. G. Karol D. A. Baum M. W. Chase S. M. Swensen R. McCourt K. J. Sytsma (1998) ArticleTitleCircumscription of the Malvales and relationships to other Rosidae: evidence from rbcL sequence data Amer. J. Bot. 85 876–887 Occurrence Handle1:CAS:528:DyaK1cXktlCltLs%3D Occurrence Handle10.2307/2446423
Anonymous (1991) Kebun percobaan Haurbentes, Jasinga. Badan Penelitian dan Pengembangan Kehutanan, Departemen Kehutanan, Jakarta.
APG - The Angiosperm Phylogeny Group (2003) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Bot. J. Linn. Soc. 141: 399–436.
P. S. Ashton (1982) Flora malesiana, series I – Spermatophyta, flowering plants, vol. 9, part 2, Dipterocarpaceae Martinus Nijhoff The Hague, Boston, London
Awasthi N. (1996) Dipterocarps in the Indian subcontinent: past, present and future. In: Appanah S., Khoo K. C. (eds.) Proceedings of the fifth round-table conference on dipterocarps. Chiang Mai. 7–10 November 1994, pp. 138–156
H. Bancroft (1933) ArticleTitleA contribution to the geological history of the Dipterocarpaceae Geol. Fören. Förhandl. 55 59–100
H. Bancroft (1935) ArticleTitleSome fossil dicotyledonous woods from Mount Elgon, East Africa. I. Amer. J. Bot. 22 164–183 Occurrence Handle10.2307/2436007
N. G. Bisset M. A. Diaz-Parra C. Ehret G. Ourisson M. Palmade F. Patil P. Pesnelle J. Streith (1966) ArticleTitleÉtudes chimio-taxonomiques dans la familie des Diptérocarpacées – II Constituants du genre Dipterocarpus Gaertn. F. Essai de classification chimio-taxonomique Phytochemistry 5 865–880 Occurrence Handle1:CAS:528:DyaF2sXkvFU%3D Occurrence Handle10.1016/S0031-9422(00)82783-1
M. T. Clegg B. S. Gaut G. H. Learn B. R. Morton (1994) ArticleTitleRates and patterns of chloroplast DNA evolution Proc. Natl. Acad. Sci. USA 91 6795–6801 Occurrence Handle8041699 Occurrence Handle1:CAS:528:DyaK2cXlslehsb4%3D Occurrence Handle10.1073/pnas.91.15.6795
U. M. Csaikl H. Bastian R. Brettschneider S. Gauch A. Meir M. Schauerte F. Scholz C. Sperisen B. Vornam B. Ziegenhagen (1998) ArticleTitleComparative analysis of different DNA extraction protocols; a fast, universal maxi-preparation of high quality plant DNA for generic evaluation and phylogenetic studies Pl. Molec. Biol. Rep. 16 69–86 Occurrence Handle1:CAS:528:DyaK1MXjs1Ortbk%3D Occurrence Handle10.1023/A:1007428009556
Danimihardja S., Notodihardjo D. (eds.) (2001) An alphabetical list of plant species cultivated in the Hortus Botanicus Bogoriensis. Botanic Gardens, National Biological Institut, Indonesian Institute of Sciences, Bogor
S. Dayanandan P. S. Ashton S. M. Williams R. B. Primack (1999) ArticleTitlePhylogeny of the tropical tree family Dipterocarpaceae based on nucleotide sequences of the chloroplast rbcL gene Amer. J. Bot. 86 1182–1190 Occurrence Handle1:CAS:528:DyaK1MXlvFals7c%3D Occurrence Handle10.2307/2656982
Ducousso M., Béna G., Bourgeois C., Buyck B., Eyssartier G., Vincelette M., Rabevohitra R., Randrihasipara L., Dreyfus B., Prin Y. (2004) The last common ancestor of Sarcolaenaceae and Asian dipterocarp trees was ectomycorrhizal before the India-Madagascar separation, about 88 million years ago. Molec. Ecol. 13: 231.236.
D. T. Gamage M. Silva Particlede A. Yoshida A. E. Szmidt T. Yamazaki (2003) ArticleTitleMolecular phylogeny of Sri Lankan Dipterocarpaceae in relation to other Asian Dipterocarpaceae based on chloroplast DNA sequences Tropics 13 79–87
H. Gottwald N. Parameswaran (1966) ArticleTitleDas sekundäre Xylem der Familie Dipterocarpaceae Bot. Jahrb. Syst. 85 410–508
Hallé F. (1979) Premières donnees architecturales sur les Dipterocarpaceae. In: Maury-Lechon G. (ed.) Diptérocarpacées, Taxonomie-Phylogénie-Écologie. Mémoires du Muséum National d'Histoire Naturelle. Paris. Series B, Botanique 26: 20–34.
T. Kajita K. Kamiya K. Nakamura H. Tachida R. Wickneswari Y. Tsumura H. Yoshimaru T. Yamazaki (1998) ArticleTitleMolecular phylogeny of dipterocarpaceae in Southeast Asia based on nucleotide sequences of matK, trnL intron, and trnL-trnF intergenic spacer region in chloroplast DNA Molec. Phylogenet. Evol. 10 202–209 Occurrence Handle9878231 Occurrence Handle1:CAS:528:DyaK1MXktlKqsQ%3D%3D Occurrence Handle10.1006/mpev.1998.0516
K. Kamiya K. Harada K. Ogino T. Kajita T. Yamazaki H. S. Lee P. S. Ashton (1998) ArticleTitleMolecular phylogeny of dipterocarp species using nucleotide sequences of two non-coding regions in chloroplast DNA Tropics 7 195–207 Occurrence Handle10.3759/tropics.7.195
K. Kamiya K. Harada H. Tachida P. S. Ashton (2005) ArticleTitlePhylogeny of PgiC gene in Shorea and its closely related genera (Dipterocarpaceae), the dominant trees in Southeast Asian tropical rain forests Amer. J. Bot. 92 775–788 Occurrence Handle1:CAS:528:DC%2BD2MXks1WqsLo%3D
Q.-M. Li T.-H. He Z.-F. Xu (2004) ArticleTitleGeneric relationships of Parashorea chinensis Wang Hsie (Dipterocarpaceae) based on cpDNA sequences Taxon 53 461–466 Occurrence Handle10.2307/4135622
A.C. Londoño E. A. Alvarez E. Forero C. M. Morton (1995) ArticleTitleA new genus and species of Dipterocarpaceae from the Neotropics. I. Introduction, taxonomy, ecology, and distribution Brittonia 47 225–236 Occurrence Handle10.2307/2807116
B. Maguire P. S. Ashton (1977) ArticleTitlePakaramoideae, Dipterocarpaceae of the western hemisphere. II. Systematic, geographic, and phyletic considerations Taxon 26 341–385 Occurrence Handle10.2307/1220033
G. Maury-Lechon L. Curtet (1998) Biogeography and evolutionary systematics of Dipterocarpaceae S. Appanah J. M. Turnbull (Eds) A review of dipterocarps, taxonomy, ecology and silviculture Center for International Forestry Research Bogor
Meijer W. (1979) Taxonomic studies in the genus Dipterocarpus. In: Maury-Lechon G. (ed.) Diptérocarpacées, Taxonomie-Phylogénie-Écologie. Mémoires du Muséum National d'Histoire Naturelle. Paris. Series B, Botanique 26: 50–56.
R. J. Morley (2000) Origin and evolution of tropical rain forests John Wiley & Sons Chichester
C. M. Morton S. Dayanandan D. Dissanayake (1999) ArticleTitlePhylogeny and biosystematics of Pseudomonotes (Dipterocarpaceae) based on molecular and morphological data Pl. Syst. Evol. 216 197–205 Occurrence Handle10.1007/BF01084398
M. F. Newman P. F. Burgess T. C. Whitmore (1996) Manuals of dipterocarps for foresters, Borneo island light hardwoods Center for International Forestry Research Jakarta
Parameswaran N., Gottwald H. (1979) Problematic taxa in the Dipterocarpaceae, their anatomy and taxonomy. In: Maury-Lechon G. (ed.) Diptérocarpacées, Taxonomie-Phylogénie-Écologie Mémoires du Muséum National d'Histoire Naturelle. Paris. Series B, Botanique 26: 69–75.
Sist P. (1996) Structure and diversity of dipterocarps in a lowland dipterocarp forest in East Kalimantan. In: Appanah S., Khoo K. C. (eds.) Proceedings of the fifth round-table conference on dipterocarps. Chiang Mai. 7–10 November 1994, pp. 60–86.
J. W. F. Slik A. D. Poulsen P. S. Ashton C. H. Cannon K. A. O. Eichhorn K. Kartawinata I. Lanniari H. Nagamasu M. Nakagawa M. G. L. Nieuwstadt Particlevan J. Payne A. Saridan K. Sidiyasa R. W. Verburg C. O. Webb P. Wilkie (2003) ArticleTitleA floristic analysis of the lowland dipterocarp forests of Borneo J. Biogeogr. 30 1517–1531 Occurrence Handle10.1046/j.1365-2699.2003.00967.x
Swofford D. L. (1998) PAUP*, Phylogenetic analysis using parsimony (and other methods). Version 4.0. Sinauer Associates. Sunderland. Massachusetts.
Symington C. F. (1943) Malayan foresters records no. 16, Forester’s manual of dipterocarps. Penerbit Universiti Malaysia, Kuala Lumpur.
P. Taberlet L. Gielly G. Pautou J. Bouvet (1991) ArticleTitleUniversal primers for amplification of three non-coding regions of chloroplast DNA Pl. Molec. Biol. 17 1105–1109 Occurrence Handle1:CAS:528:DyaK38Xhslel Occurrence Handle10.1007/BF00037152
Y. Tsumura T. Kawahara R. Wickneswari K. Yoshimura (1996) ArticleTitleMolecular phylogeny of Dipterocarpaceae in Southeast Asia using RFLP of PCR-amplified chloroplast genes Theor. Appl. Genet. 93 22–29 Occurrence Handle1:CAS:528:DyaK28XlvFarur8%3D Occurrence Handle10.1007/s001220050242
Verdcourt B. (1989) Dipterocarpaceae. In: Polhill R. M (ed.) Flora of tropical east Africa. A.A. Balkema. Rotterdam, pp. 1–11.
Weidelt J. W., Banaag V. S. (1982) Aspects of management and silviculture of philippine dipterocarp forests. Deutsche Gesellschaft für Technische Zusammenarbeit (GTZ) GmbH Eschborn.
K. Weising R. C. Gardner (1999) ArticleTitleA set of conserved primers for the analysis of simple sequence repeat polymorphisms in chloroplast genomes of dicotyledonous angiosperms Genome 42 9–19 Occurrence Handle10207998 Occurrence Handle1:CAS:528:DyaK1MXhsVyqsb0%3D Occurrence Handle10.1139/gen-42-1-9
T. C. Whitmore (1975) Tropical rain forests of the far east Clarendon Press Oxford
A. J. Whitten S. J. Damanik J. Anwar N. Hisyam (1987) The ecology of Sumatra Gadjah Mada University Press Yogyakarta
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Indrioko, S., Gailing, O. & Finkeldey, R. Molecular phylogeny of Dipterocarpaceae in Indonesia based on chloroplast DNA. Plant Syst. Evol. 261, 99–115 (2006). https://doi.org/10.1007/s00606-006-0435-8
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00606-006-0435-8