Molecular database for classifying Shorea species (Dipterocarpaceae) and techniques for checking the legitimacy of timber and wood products

Phytochemical and pharmacological profile of genus shorea: A review of the recent literature

In tropical Southeast Asia, Shorea is the most economically important tree and the largest genus in the Dipterocarpaceae family. It comprises about 150-200 species, of which majority are distributed in Malaysia, with others found in Sumatra and Borneo (Kalimantan) in Indonesia. Research on the chemical constituents of Shorea plants has been ongoing for many years. To date, a total of 113 different compounds, including 83 stilbenes and their resveratrol oligomers, 18 triterpenes/terpenoids, 7 coumarins 3 flavonoids and 2 steroids have been isolated and successfully elucidated from 26 different species of this genus. The diversity of the stilbene resveratrol oligomers in the Shorea genus is primarily due to the difference in the amount of resveratrol constituent units, which include dimers, trimers and tetramers. In addition to the species' traditional usage in the treatment of illnesses, such as diarrhea, toothaches, skin diseases, ear troubles and wounds, the extracts and secondary metabolite compounds isolated from various parts of the plant species are known to have a very potent antioxidant, antimicrobial, anticancer, anti-diabetic, anti-obesity, antiulcer, hepatoprotective and nephroprotective activities. This review aims to summarize the most recent research made from 1999 to date on the secondary metabolite compounds isolated from different species of genus Shorea, as well as the bioactivity (in vitro and in vivo) of the crude extracts and the isolated secondary metabolite compounds.

Screening of potential chemical marker with interspecific differences in Pterocarpus wood and a spatially-resolved approach to visualize the distribution of the characteristic markers

Profiling the spatial distributions and tissue changes of characteristic compounds with interspecific differences is critical to elucidate the complex species identification during tree species traceability, wood anti-counterfeiting verification and timber trade control. In this research, in order to visualize the spatial position of characteristic compounds in two species with similar morphology (Pterocarpus santalinus and Pterocarpus tinctorius), a high coverage MALDI-TOF-MS imaging method was used to found the mass spectra fingerprints of different wood species. 2-Mercaptobenzothiazole matrix was used to spray wood tissue section to enhance the detection effect of metabolic molecules, and the mass spectrometry imaging data were obtained. Based on this technology, the spatial location of fifteen potential chemical markers with remarkable interspecific differences in 2 Pterocarpus timber species were successfully obtained. Distinct chemical signatures obtained from this method can promote rapid identification at the wood species level. Thus, matrix-assisted laser desorption/time-of-flight/ionization mass spectrometry imaging (MALDI-TOF-MSI) provides a spatial-resolved way for traditional wood morphological classification and breaking through the limitations of traditional wood identification technology.

Taxonomical Evaluation of Plant Chloroplastic Markers by Bayesian Classifier

DNA barcodes are standardized sequences that range between 400 and 800 bp, vary at different taxonomic levels, and make it possible to assign sequences to species that have been previously taxonomically characterized. Several DNA barcodes have been postulated for plants, nonetheless, their classification potential has not been evaluated for metabarcoding, and as a result, it would appear as none of them excels above the others in this area. One tool that has been widely used and served as a baseline when evaluating new approaches is Naïve Bayesian Classifiers (NBC). The present study aims at evaluating the classification power of several plant chloroplast genetic markers that have been proposed as barcodes (trnL, rpoB, rbcL, matK, psbA-trnH, and psbK) using an NBC. We performed the classification at different taxonomic levels, and identified problematic genera when resolution was desired. We propose matK and trnL as potential candidate markers with resolution up to genus level. Some problematic genera within certain families could lead to the misclassification no matter which marker is used (i.e., Aegilops, Gueldenstaedtia, Helianthus, Oryza, Shorea, Thysananthus, and Triticum). Finally, we suggest recommendations for the taxonomic identification of plants in samples with potential mixtures.

Integrating DNA Barcoding and Traditional Taxonomy for the Identification of Dipterocarps in Remnant Lowland Forests of Sumatra

DNA barcoding has been used as a universal tool for phylogenetic inferences and diversity assessments, especially in poorly studied species and regions. The aim of this study was to contrast morphological taxonomy and DNA barcoding, using the three frequently used markers matK, rbcL, and trnL-F, to assess the efficiency of DNA barcoding in the identification of dipterocarps in Sumatra, Indonesia. The chloroplast gene matK was the most polymorphic among these three markers with an average interspecific genetic distance of 0.020. The results of the molecular data were mostly in agreement with the morphological identification for the clades of Anthoshorea, Hopea, Richetia, Parashorea, and Anisoptera, nonetheless these markers were inefficient to resolve the relationships within the Rubroshorea group. The maximum likelihood and Bayesian inference phylogenies identified Shorea as a paraphyletic genus, Anthoshorea appeared as sister to Hopea, and Richetia was sister to Parashorea. A better discriminatory power among dipterocarp species provided by matK and observed in our study suggests that this marker has a higher evolutionary rate than the other two markers tested. However, a combination of several different barcoding markers is essential for reliable identification of the species at a lower taxonomic level.

Using a mega-phylogeny of seed plants to test for non-random patterns of areal-types across the Chinese tree of life

The species composition of plant assemblages can in large part be explained by a long history of biogeographic and evolutionary events. Over the past decade, botanists and plant ecologists have increasingly sought to quantify phylogenetic signal in ecological traits to help inform their inferences regarding the mechanisms driving plant assemblages. However, most studies with a test of phylogenetic signal in the ecological traits have focused on a local scale, while comparatively few studies have been carried out on a regional scale. In this study, I presented a family-level phylogeny and a genus-level phylogeny that included all families and genera of extant seed plants in China, and use both phylogenies to examine whether areal-types or distribution patterns of families and genera of seed plants are non-randomly distributed across the Chinese tree of life. My study shows that the areal-types of families and genera of seed plants exhibit significant phylogenetic signal across the family- or genus-level phylogeny of seed plants in China.

Phylogeographical pattern and evolutionary history of an important Peninsular Malaysian timber species, Neobalanocarpus heimii (Dipterocarpaceae)

Tectonic movements, climatic oscillations, and marine transgressions during the Cenozoic have had a dramatic effect on the biota of the tropical rain forest. This study aims to reveal the phylogeography and evolutionary history of a Peninsular Malaysian endemic tropical timber species, Neobalanocarpus heimii (Dipterocarpaceae). A total of 32 natural populations of N. heimii, with 8 samples from each population were investigated. Fifteen haplotypes were identified from five noncoding chloroplast DNA (cpDNA) regions. Overall, two major genealogical cpDNA lineages of N. heimii were elucidated: a widespread southern and a northern region. The species is predicted to have survived in multiple refugia during climatic oscillations: the northwestern region (R1), the northeastern region (R2), and the southern region (R3). These putative glacial refugia exhibited higher levels of genetic diversity, population differentiation, and the presence of unique haplotypes. Recolonization of refugia R1 and R2 could have first expanded into the northern region and migrated both northeastwards and northwestwards. Meanwhile, recolonization of N. heimii throughout the southern region could have commenced from refugia R3 and migrated toward the northeast and northwest, respectively. The populations of Tersang, Pasir Raja, and Rotan Tunggal exhibited remarkably high haplotype diversity, which could have been the contact zones that have received an admixture of gene pools from the northerly and also southerly regions. As a whole, the populations of N. heimii derived from glacial refugia and contact zones should be considered in the conservation strategies in order to safeguard the long-term survival of the species.

Contrasting cpDNA variation in two Indonesian endemic lowland dipterocarp species and implications for their conservation

Shorea javanica (Dipterocarpaceae) is an economically important dammar-producing tree, endemic to the tropical lowland forests of Sumatra and Java, Indonesia. However, its total population size is limited and this species is endangered. Shorea selanica is one of the very limited numbers of species in genus Shorea (Dipterocarpaceae) that grows in Wallacean. This species can be found only in the central part of the Moluccas, eastern Indonesia. Six populations (77 individuals in total) were sampled for S. javanica while three populations (27 individuals in total) were sampled for S. selanica. To determine genetic variation and population structure, three non-coding chloroplast DNA regions of trnL-trnF, psbC-trnS, trnS-trnfM and two non-coding chloroplast DNA regions of trnT-trnL, trnL-trnF were sequenced from S. javanica and S. selanica, respectively. There was no variation in the chloroplast DNA regions from S. javanica, except for one unique indel polymorphism. Nucleotide diversity within S. selanica populations ranged from 0 (Seram) to 0.00044 (Buru), with a pooled value of 0.00041. S. javanica was determined as having no population structure while high levels of genetic differentiation was found among populations of S. selanica (F(ST) = 0.702). Different pattern of population structure among the two species in this study suggested the need for distinct management and conservation strategies for each species. For S. javanica, connectivity within and among populations, including augmentation of population size across the species range, should be promoted. For S. selanica, an in situ conservation plan that defines core areas completely free from perturbation within each population is necessary.