Molecular phylogeny of Dipterocarp Species Using Nucleotide Sequences of Two Non-coding Regions in Chloroplast DNA.

Kamiya, Katsumasa; Harada, Ko; Ogino, Ken; Kajita, Tadashi; Yamazaki, Tsuneyuki; Lee, Hua-Seng; Ashtion, Peter Shaw

doi:10.3759/tropics.7.195

Cited by 26 publications

(38 citation statements)

References 11 publications

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“…The generic relationships revealed by our NJ tree are mostly in agreement with previous molecular phylogenies based on cpDNA Gamage et al, 2003;Kajita et al, 1998;Kamiya et al, 1998). However, our current results provide new evidence regarding the relationships of additional genera such as Monotes, Vateriopsis and Stemonoporus, which were not included or discussed well (except Monotes) in most previous studies Kamiya et al, 1998).…”

Section: Generic Relationshipssupporting

confidence: 80%

“…Since then, several other phylogenetic studies on Dipterocarpaceae were reported based on chloroplast (cp) DNA sequences Gamage et al, 2003;Kajita et al, 1998;Kamiya et al, 1998;Morton et al, 1999) and the nuclear gene PgiC (Kamiya et al, 2005). However, previous studies on molecular phylogeny of the Dipterocarpaceae included either limited number of species Morton et al, 1999;Tsumura et al, 1996) or informative sites (Gamage et al, 2003;Kamiya et al, 1998) or both . The most recent work by Kamiya et al (2005) has mainly focused on the relationships of Shorea , Hopea, Neobalanocarpus and Parashorea genera and did not include species from the Dipterocarpeae tribe and species of the Doona genus (Kostermans, 1984;Kostermans, 1992;Maury, 1978;Maury-Lechon, 1979).…”

Section: Introductionmentioning

confidence: 99%

“…In addition to sequences obtained in the present study (24 sequences for trnL-trnF spacer and trnL intron regions and 65 sequences for matK ), we used data reported in the previous studies (Table 1). For the trnL-trnF spacer and trnL intron regions we used seven sequences obtained by Kamiya et al (1998), 34 sequences obtained by Gamage et al (2003) and 14 sequences reported by Kajita et al (1998). For the matK region, we used 14 sequences from Malaysian species reported by Kajita et al (1998) Vatica affinis Thw.…”

Section: Species Samplingmentioning

confidence: 99%

“…For the trnL-trnF spacer and trnL intron regions sequencing primers were the same as those used for PCR, while sequencing primers designed by Kajita et al (1998) and newly designed PCR and internal primers were used for sequencing of the matK region (Table 2). Nucleotide sequence data obtained in this study and the sequences used by Kamiya et al (1998) are diposited in the DDBJ/EMBL/GenBank databases under accession numbers AB246414 through AB246478, AB246479 through AB246543 and AB246544 through AB246608 for the matK, trnL-trnF, and trnL intron regions respectively.…”

Section: Species Samplingmentioning

confidence: 99%

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Comprehensive Molecular Phylogeny of the Sub-Family Dipterocarpoideae (Dipterocarpaceae) Based on Chloroplast DNA Sequences

et al. 2006

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Dipterocarpoideae, the largest sub-family of well-known plant family Dipterocarpaceae, dominates in South Asian rain forests. Although several previous studies addressed the phylogeny of the Dipterocarpaceae family, relationships among many of its genera from the Dipterocarpoideae sub-family are still not well understood. In particular, little is known about the relationships of the genera Vateriopsis , Stemonoporus , Vateria and inconsistence remains between phylogenetic results and taxonomic classifications of Shorea and Hopea species. We studied molecular phylogeny of the sub-family Dipterocarpoideae using the trnL-trnF spacer, trnL intron and the matK gene sequences of chloroplast DNA (cpDNA). This study is the first comprehensive phylogeny reconstruction for the sub-family Dipterocarpoideae based on cpDNA, as it includes most genera (14) and a large number of species (79) with most species endemic to Sri Lanka, as well as one species from Seychelles and one species from the genus Monotes from Madagascar. Phylogenetic trees were constructed using the Neighbor Joining (NJ) and Maximum Likelihood (ML) methods using combined set of sequences including all three cpDNA regions. The topologies of the NJ and ML trees were to a certain extent, consistent with the current taxonomy of Dipterocarpoideae based on morphology and with previous molecular phylogenies based on cpDNA. Furthermore, our results provided new evidence regarding the relationships of the following genera: Vateriopsis and Stemonoporus and about the validity of the previous morphology based classifications of Shorea species. In addition, the topology of our trees was consistent with the classification of Shorea species proposed by Maury (1978), Maury-Lechon (1979) and Symington (1943). Finally, our results provided evidence for the affinity of the genus Monotes to Asian Dipterocarpoideae rather than to Tiliaceae and indicated that it is a good candidate for outgroup species for future studies of the former sub-family.

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Section: Generic Relationshipssupporting

confidence: 80%

Section: Introductionmentioning

confidence: 99%

Section: Species Samplingmentioning

confidence: 99%

Section: Species Samplingmentioning

confidence: 99%

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Comprehensive Molecular Phylogeny of the Sub-Family Dipterocarpoideae (Dipterocarpaceae) Based on Chloroplast DNA Sequences

et al. 2006

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“…The findings of this study will be used for effective management of biodieversity resources. The genetic variation and genetic relationships of tree populations in Sarawak using molecular markers, such as RAPD, AFLP, microsatellite and DNA sequencing were studied (Harada et al, 1994;Kamiya et al, 1998 of organisms, the genetic constitution of tree populations could be objectivity determined if proper molecular makers are used, that is, the analysis of DNA variations could provide more conclusive results for studies on phylogeny and population genetics of organisms, than indirect observation of genetic variation using morphology and proteins (Nei, 1987). Moreover, it is also mentioned that because much of the research today uses PCR (polymerase chain reaction) DNA material should be qualified for the method (Mullis & Faloona, 1987).…”

Section: Introductionmentioning

confidence: 99%

Construction of a gene-data bank of tropical rainforest tree species in Sarawak, Malaysia

Konishi

Harada

Chong

et al. 2003

Tropics

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A "gene-data bank" of tropical rainforest tree species in Sarawak was constructed. This work was initiated to deposit DNA materials from tree species in the whole area of Sarawak and found the information gathered to be effective tools for the sustainable management of bio-resources. For this study leaf samples, mainly from dipterocarp species, were collected from eight natural populations in national parks mainly and also several man-made forests. We collected nearly 5,000 samples including 127species in 27 families. DNA extraction was done in the Forest Research Centre (FRC) in Kuching, Sarawak using a modified CTAB method. These DNA samples were deposited along with field sampling data and DNA extraction data. Genetic analysis using RAPD, AFLP, microsatellite and DNA sequencing is now under progress to clarify the genetic constitution of the tree populations. Genetic information obtained by these methods will be useful in specifying the individual trees and will be incorporated into the gene-data bank.

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Phylogenomics and a revised tribal classification of subfamily Dipterocarpoideae (Dipterocarpaceae)

Cvetković

Hinsinger

Thomas

et al. 2022

TAXON

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Dipterocarpoideae, the largest subfamily in the Meranti family (Dipterocarpaceae) are an ecologically dominant group of trees throughout much of wet tropical Asia. Increasing anthropogenic pressures on this economically important tree family make it essential to resolve their complex evolutionary relationships and understand the distribution of genetic diversity throughout the family and distribution range. Dipterocarpaceae have been the focal group in a wide range of studies, owing to their economic value, importance in historical biogeography and key role in the evolution of the Asian tropical forest biome. Despite this, persistent taxonomic and evolutionary questions remain, ranging from questions on the geographic origin, sequence of dispersal and the identification of diagnostic characters to circumscribe proper evolutionary groups. Here we present a comprehensive phylogenomic hypothesis for Dipterocarpoideae, based on the analyses of plastome and nuclear cistron (NRC) data, and provide an in‐depth review on the validity of morphological characters underlying the new tribal classification proposed here for the subfamily. Phylogenomic relationships were inferred using maximum likelihood and Bayesian approaches. Estimates of origin and onset of diversification in major clades and lineages were reconstructed using plastome, nuclear and combined datasets. Results of the separate and combined genomic datasets partly corroborate elements of previous classification systems (with improved support at all levels for major clades) but provide strong support for revising the tribal classification of the subfamily into four main clades: Dipterocarpeae (Dipterocarpus), Dryobalanopseae (Dryobalanops), Shoreeae (Hopea, Neobalanocarpus, Parashorea, and all parts of a polyphyletic Shorea) and Vaterieae (including all other presently accepted Dipterocarpoideae genera). Multi‐fossil‐dated divergence time estimation suggests Vaterieae first originated in the Late Cretaceous, followed by Dipterocarpeae, with subsequent rise of the Dryobalanopseae and Shoreeae in the Eocene. Diversification of all tribes commenced before the Early Miocene. Our results provide strong support for the position of Neobalanocarpus heimii, Parashorea and (sub‐)sections of the genera Anisoptera, Hopea, Shorea and Vatica. Hypotheses on the origin of Neobalanocarpus heimii by intergeneric hybridisation between Anthoshorea (maternally inherited) and Hopea (paternally inherited) species were corroborated. Finally, our study provides support for future revisionary changes: (1) the elevation to generic rank of sections in Shorea; and (2) revising the infrageneric classification of Hopea as all (sub‐)sections were recovered as not monophyletic.

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Molecular phylogeny of Dipterocarp Species Using Nucleotide Sequences of Two Non-coding Regions in Chloroplast DNA.

Cited by 26 publications

References 11 publications

Comprehensive Molecular Phylogeny of the Sub-Family Dipterocarpoideae (Dipterocarpaceae) Based on Chloroplast DNA Sequences

Comprehensive Molecular Phylogeny of the Sub-Family Dipterocarpoideae (Dipterocarpaceae) Based on Chloroplast DNA Sequences

Construction of a gene-data bank of tropical rainforest tree species in Sarawak, Malaysia

Phylogenomics and a revised tribal classification of subfamily Dipterocarpoideae (Dipterocarpaceae)

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