Koichi Kamiya

Hopea celebica Burck is an endangered dipterocarp endemic to Sulawesi, Indonesia, occurring in two ecologically contrasting habitats: karst and ultrabasic forests. These environments differ markedly in soil composition and topography, potentially driving ecological specialization and genetic divergence. To investigate the genetic variation and genetic structure of this species, we applied newly developed microsatellite (SSR) markers, together with the chloroplast DNA sequences of the trnL–trnF region. Genotypes at 15 SSR loci were determined for 255 individuals collected from six populations covering the range of the species’ distribution across karst and ultrabasic forests. Genetic diversity was consistently higher in karst than in ultrabasic populations. DIYABC and VarEff analyses revealed a historical bottleneck and earlier recovery in the karst populations. Analysis of molecular variance (AMOVA) revealed that 35% of the genetic variation was partitioned between habitat types (F_RT = 0.345, p = 0.001). Bayesian clustering (STRUCTURE), principal coordinate analysis (PCoA), and UPGMA dendrograms consistently showed two distinctive clusters corresponding to habitat type. Chloroplast haplotypes differed between populations in the karst and ultrabasic forests. These results suggest that populations in the karst and ultrabasic forests have undergone a long history of differentiation without migration. The strong habitat-related genetic structure likely reflects ecological isolation and early-stage speciation. We recommend treating the karst and ultrabasic populations as distinct conservation units to preserve the evolutionary potential and adaptive capacity of H. celebica under ongoing environmental change.

The Dipterocarpaceae family comprises the dominant tree species of Southeast Asia’s rainforests, with their centre of diversity in Borneo (Kalimantan) and Sumatra, Indonesia. Despite considerable molecular research on dipterocarps, a comprehensive mapping of the research foci remains lacking. This study aims to identify research priorities, existing gaps, and methodological trends in Dipterocarpaceae studies within Indonesia to inform future research efforts, shape policy directions, and contribute to global sustainable forest management. Through two distinct searches in the Scopus database, 1174 articles were retrieved for bibliometric analysis, and 94 molecular and genetic research articles were selected according to specific keywords and criteria. Bibliometric and thematic analyses revealed two primary clusters within global studies of Dipterocarpaceae: ecology, forestry, and conservation; and phytochemistry and pharmaceutical applications. However, genetic research is primarily focused on species of notable commercial significance, specifically Rubroshorea leprosula (Miq.) P.S.Ashton & J.Heck. and Rubroshorea parvifolia (Dyer) P.S.Ashton & J.Heck. Notably, molecular and genetic research on Dipterocarpaceae in Indonesia is approximately two decades behind prevailing global trends. The current focus of molecular research in Indonesia is directed towards genetic diversity and population structure, with strong international collaborations but fragmented national networks, highlighting the need to diversify themes and strengthen partnerships. Furthermore, studies on endemic and threatened species are scarce. The findings of this study emphasize the critical need to strengthen national research capacity, advance technological development, and foster both domestic and international collaborations to address these significant knowledge gaps in the global conservation of Dipterocarpaceae.

Nasri, Kamiya K, Shimamura T, Ichie T. 2025. Karst-specific distribution of endangered Hopea celebica in Bantimurung Bulusaraung National Park, Sulawesi. Biodiversitas 26: 5395-5404. Hopea celebica is an endangered tree species endemic to Sulawesi, Indonesia, with limited ecological information available on its habitat preferences. This study aimed to investigate its distribution and habitat association in karst and non-karst areas of Bantimurung Bulusaraung (Babul) National Park, South Sulawesi, Indonesia. Seedlings, saplings, and adult trees were counted in 36 plots (50×20 m) selected using purposive sampling (18 plots in karst and 18 in non-karst areas). Elevation, slope, and canopy cover, were measured in each plot, and soil samples were analyzed for nutrient content and texture. Hopea celebica occurred exclusively in karst areas (12 of 18 plots), particularly in porous and massive karst types, showing a clumped distribution (?²: 36, p3, p<0.001). Generalized Linear Model (GLM) and Principal Component Analysis (PCA) showed that H. celebica was positively associated with steeper slope, higher soil pH, and denser canopy, but negatively with elevation. These findings highlighted porous and massive karst areas as key habitats, characterized by well-drained conditions at lower elevation, with healthy regeneration (inverted J-shaped diameter class distribution). This study suggests the need to protect porous and massive karst zones to ensure the long-term survival of H. celebica populations.

Mufarhatun N, Susilowati A, Hilwan I, Arrofaha N, Yulita KS, Dwiyanti FG, Hidayat A, Kamiya K, Rachmat HH. 2023. Leaf morphological traits of nine major tropical trees of Shorea species (Dipterocarpaceae). Biodiversitas 24: 1704-1712. Shorea is the largest genus in the Dipterocarpaceae family and has high leaf morphological variations among its species, which causes difficulties in field identification. Therefore, information on the specific characteristics of the leaf morphology of each species is needed. This study aimed to examine and discriminate leaf morphological traits at both mature and sapling stages of nine Shorea species, namely Shorea balangeran (Korth.) Burck, S. leprosula Miq., S. mecistopteryx Ridl., S. multiflora (Burck) Symington, S. ovalis (Korth.) Blume, S. pinanga Scheff., S. platyclados Slooten ex Endert, S. selanica (Wight & Arn.) Blume, and S. stenoptera Burck. The leaves of 90 mature trees growing in the Dramaga Research Forest (DRF) and Gunung Dahu Research Forest (GDRF) as well as the leaves of 180 saplings growing in the nursery of Forest Research and Development Center (FRDC) were observed. Leaf traits, leaf color, and chlorophyll content were assessed on 3 leaves from each mature tree and 5 from each sapling collected. Furthermore, comparative analysis using F independent test in the one-way analysis variance (ANOVA), multivariate analysis using Principal Component Analysis (PCA), and Hierarchical Cluster Analysis were used in this study. The results showed that 8 of the 11 measured morphological traits were identified as the quantitative leaves morphological differentiators, namely Leaves Width (LW), Lamina Length (LL), the length between the largest Leaves Point (LP) with the base of the leaves, angle of leaves vein (SD), Petiole Length (PL), number of leaves vein (LB), breadth of the leaves (WL), and the Circumference of the Leaves (CL). In addition, the results of cluster analysis showed the nine Shorea spp. are clustered into two major groups. Group 1 consisted of species, S. stenoptera, and S. mecistopteryx, while the remaining are included in Group 2. Our findings conclude that the eight leaf morphological traits obtained from this study are useful as additional characters to distinguish the nine Shorea species in the field.

Conservation of rare species is essential for maintaining ecosystem function. Quercus hondae is a rare evergreen oak species (Cyclobalanopsis) endemic to Japan. This species is found in several locations in Southwestern Japan; small populations remain in the tutelary forests of the Japanese shrine. To evaluate the genetic diversity and phylogeographic structure of this rare species, 11 microsatellite loci and chloroplast DNA sequences are analyzed for 12 populations of Q. hondae and 8 populations of the more widespread congeneric species, Q. glauca. It is found that heterozygosity at both the population and species level is substantially lower in Q. hondae than in Q. glauca. Genetic differentiation among populations of Q. hondae was high, in contrast to Q. glauca, in which populations exhibit largely insignificant differentiation. STRUCTURE analysis shows that at K = 7, the clusters largely corresponded to major predefined populations. This study suggests that there is little gene flow among extant Q. hondae populations and that Q. hondae is genetically differentiated due to the greater effect of genetic drift in small populations. This pattern is in sharp contrast to that of a more common congeneric species, which will be an important consideration in the conservation of Q. hondae.

Shabrina H, Siregar UJ, Matra DD, Kamiya D, Siregar IZ. 2019. Short Communication: DNA extraction from stored wood of Falcataria moluccana suitable for barcoding analysis. Biodiversitas 20: 1748-1752. Sengon or Falcataria moluccana (Miq.) Barneby & J.W.Grimes is the main crop in community tree plantations in Java, Indonesia, favored because of its fast-growing property and the promising economic return. The wood itself is mostly used for light construction, furniture, plywood, packing materials, and recently as feedstock for bioenergy. Sometimes the wood is used as DNA source for example in the wood identification analysis. However, extracting DNA from woods is considered difficult due particularly to very small quantities of DNA. The objective of this research was to optimize and modify the common CTAB protocols to extract DNA from Sengon wood without liquid nitrogen which sometimes unavailable in some laboratories. The extracted DNA was quantified with nanophotometer and gel visualization and amplified with primer coding psbA-trnH intergenic spacer for testing. The highest concentration of DNA extracted was from 100 mg of wood stored for 24 hours in -30 °C (257.80 ng/µL or 14.18 µg in total) and even the lowest concentration produced by this method able to produce sufficient amount of PCR product for sequencing. Compared with results from 200 mg samples and longer freezing time (72 hours) and extraction using liquid nitrogen, this method considered gave the best results.