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Molecular Phylogeny of Dtpterocarp Specles Ustng Nucleotlde Sequences of Trro Non-Codrng Regtons Rn Chloroplast DNA

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Molecular Phylogeny of Dtpterocarp Specles Ustng Nucleotlde Sequences of Trro Non-Codrng Regtons Rn Chloroplast DNA TROPICS Vol. 7 Qlg:795-207 Issued May 1998 Molecular Phylogeny of Dtpterocarp Specles Ustng Nucleotlde sequences of Trro Non-codrng Regtons rn Chloroplast DNA Koichi KAMIYA & Ko HAIIi{DA College of Agriculture, Ehime University, Matsuyama 790-(D05, Japan Kazuhiko OGINO School of Environmental Science, University of Shiga Prefecture, Hikone 522,-8533, Jryan Thdashi K,Urm Bohnical Gardens, Graduate School of Science, Univenity of Tokyo 112-0001, Japan Tbuneyuki YAII{AZAKI Department of Biology, Faculty of Science, Kyushu Univenity, Fukuoka 81}0053, Japan Hua-Seng LEf Departrnent of Forestry,93660 Kuching Sarawak, Malaysia Peter Shaw ASHTION Harvard Institute for International Development, Cambridge, MA 02138, USA ABSTRACT A total of 53 dipterocarp species belonging to ten genera were studied to examine phylogenetic relationships using the sequences of iwo non-coding regions in chloroplast DNA. Phylogenetic analysis showed the Selangan Batu, Yellow Meranti and While Meranti of the genus Shorea were monophyletic, while the Red Meranti was divided into three nalural clades. The relationships in the Red Meranti could not be ascertained because of an insufficient number ofnucleotide substitutions. The White Meranti was cluslered with sect. Pentacme and siluated in an outer position of the gems Hopea, Neobalanocarpus and Parashorec although the bootstrap probability was not high. Two of the three deciduous Shorea species collected in Thailand, one belonging lo White Meruti and the other to sect. Pentacme based on morphological and anatomical evidence, were found to constitute a monophyletic group clustering with the other White Meranties. The third species in the Selangan Batu was clustered with the other Selangan Batus. This suggests that the deciduous character in the genus Shoreahas evolved independently in differentlineages. The divergence within sections of the genus Sftorea was largest in sed. Mutica and smallest in sect. Richetioides. The genera Shorea and Hopea werc more divergenl than the other genera. These resulls suggest that they are the groups of phylogenetically more diversified species. Key lVords: molecular phylogeny / dipterocarp species / genus Shorea I chloroplast DNA / trnLtrnF intergenic spacnr region / trnL intron Dipterocarpaceae is subdivided into three subfamilies: Dipterocarpoideae, Monotoideae and Pakaraimoideae (Ashton, 1.982). Monotoideae is represented in Africa, Madagascar and South America by three genera. The monotypic genus Palwraimaea is placed in the Pakaraimoideae and is distributed throughout the lower slopes of Guyana Highlands, South America. Dipterocarpoideae is the largest subfamily and distributed throughout Malesia which is a biogeographical region including Malaysia, Indonesia, Philippines, Singapore, Brunei and Papua New Guinea. It includes L3 genera and 470 species (Symington, 1.943; Ashton, l98Z). Subfamily Dipterocarpoideae is classified into two tribes, Dipterocarpeae and Shoreae, primarily on the basis of chromosome number, the nature of the fruit sepals and wood anatomy (see Ashton, 1982). Out of the 13 genera, Shorea is the largest genus of Dipterocarpaceae. It consists of about 194 species and 163 of which occur in Malesia (Newman et al., 1996). The division of Slorea into four 196 K. Karr,rly4 K. HanapA, K. OcINo, T. KenrA, T. YeuezeKl, H.-S. Lne & P. S. AsHroN major timber groups (Selangan Batu, White Meranti, Yellow Meranti and Red Meranti) agrees roughly with the division of the genus into sections (Newman, 1996). Ashton (1982) subdivided Shorea into ten sections mainly by the morphological features of the flower, more often by caryx lobe and wood anatomy. Tsumura et al. (1996) reported a phylogenetic study of 30 dipterocarp species using the restriction fragment length polymorphism (RFLP) of some genes of chloroplast DNA. These species were clearly separated into two species groups that correspond to two different basic chromosome numbers: the first group with n=7 and the other with n=11.. Their results agreed with the classification made by Ashton (1982). Moreover, their data indicated that Slprea bracteolata md S. singkawazg were closer to Hopea than to the other Shorea species. They suggested that Shorea is heterogeneous and its validity should be reexamined. They could not clearly show the infrageneric relationships of Slnrea because of insufficient number of polymorphic sites and the limited number of species studied. Here we constructed a phylogenetic tree in Dipterocarpaceae, mainly the genus Shorea to clarify the genetic relationships using direct sequencing of two non-coding regions in chloroplast DNA. The use of sequencing directly the amplified products of PCR is now expanding in plant systematics. DNA sequencing can provide a large data sets of discrete characters such as nucleotide substitutions, insertions and deletions (indels) and other structural changes (Gielly & Taberlet 1.994, Johnson & Soltis 1994). The goals of our study are thus two-fold: Firstly to determine the extent of chloroplast DNA divergence among dipterocarp species. Secondly to construct a molecular phylogenetic tree and compare it with the morphological classifications made by Ashton (1982\. In addition, we intend to clarify the relationships between the genera Shorea and Hopea, and the infrageneric relationships within the genus Shorea. MATERIALS AND METHODS Materials I-eaf samples were obtained in a canopy biology plot of 8-ha and a long term ecological research plot of 52-ha at l,ambir Hills National Park, Sarawak, Malaysia. In the center of the canopy biology plor, all trees with diameter at breast height (DBH) more than L0cm were tagged and recorded by Ohkubo er a/.(personal communication). In the long term ecological research plot, all trees with DBH more than lcrn were tagged and recorded by Ia Frankie et al. (personal communication). Samples were collected from 36 tree species in five genera in August 1995 and August 1996. t€af samples were identified by the author (K. K.) by compairing with the specimens deposited in the laboratory of Lambir Hills National Park whose duplicates were deposited in the herbarium of the Forest Department of Sarawak in Kuching (personal communication by Momose er a/.). Five species (Dipterocarpus alatus, Hopea odorata, Shorea obtusa, S. roxburghii and S. siamensis) were collected at the Botanical Garden in Hae Kew, Chiang Mai, Thailand in January L996. Nucleotide sequences from 1,2 species (Cotylelobiutn lanceolatwn, Anisoptera laevis, A. thurifera ssp. thurifero, A. costata, Neobalanocarpus heimii, Parashorea lucida, Dipterocarpus baudii, D. kerrii, Upuna borneensis, Dryobalanops oblongifulia, Shorea bracteolata and, Hopea nertosa\ were cited from Kajita et al. (1997 , in press). These species were collected at the Forest Research Institute of Malaysia (FRIM) arboretum and nursery. Voucher specimens collected here are deposited in FRIM herbarium. The information on each species is shown in Table 1. Molecular phylogeny of dipterocarp species 197 Table 1. Species analyzed with their section, subsection names and sources. Species Field group Section* Subsection* Source** Shormbimpak Selangan Batu Shorm Barbata A Shorm exelliptica Shorea A Shorea falciferoides A Shorm geniculata A Shorea hnailandii A Shorm superba A Shorea obtusa B Shorm agami White Meranti Anthoshorea A Shorea bracteolata c Shorea ochracea A Shorea racburghii A Shorea faguetiann YellowMeranti Richetoides Riclutoides A Shorea laxa A Shorm patoicnsis A Shorea xanthophylla A Shoreabullata Red Meranti BraclrySptuae Braclryptqae A Shorm fallax A Shorm pauciflora A Shorea acuta Mutica Auriculatae A Shorm ferruginea A Shoren argentifolia Mutica A Shorea curtisii A Shor ea mncropter n ssp . rwcropt uifolin A Shorm ouata A Shorea pantifolia A Shorea qundrinerais A Shorea rubra A Shorea oaalis Oaalis A Shoreabeccarinna Pachycarpa A Shorea macrophylla A Shorea pilosa A Shorea sinmensis Pentacme Parashorea lucida Hopea dryobalanoides A Hopea grffithii A Hopu neraosa C Hopea odorata B N eob aI ano cnrp us heimii Dry ob alan ops ar omat ic a A Dry ob al an op s lanc e olat a A D ry ob al an op s oblo n gifo Ii a C Dipterocarpus alatus B Dipterocarpus baudii C Dipterocarpus kerrii C Dipt er o car pus palembanicus ssp . borneensis A Upuna borneensts Vatica micrmttha A Vatica oblongifolia A Vatica sarmar*ensis A Anisoptera laeuis C Anisopter a tlwr ifera ssp, tln r ifera c Anisoptera costata C C o ty I eI ob ium Inn c e o latum * The sections and subsections were cited from Ashton (1982). ** A: Lambir National Park, Sarawak, Malaysia. B: Botanical Gardery Haw Kew, Chiang Mai, Thailand. C: Cited from Kajita et al. (in press). 198 K. KarraryA, K. HennnA, K. OGrNo, T. KerrrA, T. YauazeKr, H.-S. LEE & P. S. AsrroN DNA isolation and purilication Total DNA was isolated from living leaf tissues following the method of Terauchi (199a). The isolated DNA was dissolved into 400p1 of TE buffer (10mM Tris-HCl, pH7.5, 1mM EDTA ,pH8.0). For some species, total DNA was extracted from dried leaf tissues following the protocols of the CTAB method (Doyle & Doyle, 1990) with minor modification. Approximately 0.5-1.09 of leaf tissue were used for DNA isolation. The DNA was washed with 70Vo ethanol and dissolved into 500U,1 of TE buffer. Two pl of l0mg/ml RNaseA was added and incubated at37"C for t hour. The DNA solution was further purified by extraction using an equal volume of Tris-saturated phenol several times. The DNAwas dissolved into 20 to 100u1 of TE buffer. PCR amplification and DNA sequencing Two non-coding regions of chloroplast DNA including an intron of trnL (UAA) and an intergenic spacer between trnL (pAA) 3' and frzF (GAA) 5' exon were amplified by PCR (polymerase chain reaction). These regions are considerably useful for evolutionary studies of closely related species (Iaberlet et al., t99l). GeneAmp PCR System 2400 (Perkin Elmer) was used for the amplification. Primers were designed by Taberlet et al. (1991) to match the conserved regions for universal use. Sequences of the two pairs of the primers for the intron and the exon were 5'- CGAAATCGGTAGACGCTACG-3' and 5'-GGGGATAGAGGGACTTGAAC-3', and 5'- GGTTCAAGTCCCTCIATCCC-3' and 5'-ATTIGA\ACTGGTGACACGAG-3', respectively (Iaberlet et al., l99l).
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