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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.

The successful isolation of DNA (Deoxyribonucleic Acid) is essential for the investigation process of forestry molecular genetics. Samples used are usually retrieved either from soft or juvenile plant organs because of their excellent DNA source. However, in certain cases, aforesaid samples are hard to obtain, as for forensic purposes. Alternatively, woods possess potential as alternative source of DNA whose extraction method has been developed with varying degrees of success. However, to date, effectiveness on tropical wood grown in Indonesia has not been widely reported. Therefore, objective of this study was to compare the results of DNA isolation of various dried and fresh wood samples by using two isolation methods: Cetyl Trimethyl Ammonium Bromide (CTAB) and Qiagen DNeasy Plant Mini Kit (QDPMK). Extraction results were visualized in agarose gels and quantified using Nanophotometer NP80 Implen which were then amplified using two universal primers: ITS and rbcL for detecting DNA signals. Extraction results from dried wood indicated no visualization in the gel, while fresh wood samples showed thick smeared bands on both extraction methods. Quantity test results denoted higher concentration in CTAB-extracted samples compared to samples extracted using QDPMK, in both types of samples, even though both resulted in optical density ratios outside the range of purity (λ260/280: 1,8–2,0 and λ260/230: 2,0, respectively). Success rates of ITS and rbcL primary amplification in dried wood samples were quite low yet outputs from the two methods did not differ significantly. Meanwhile, outcome of ITS and rbcL amplification on fresh wood samples had a fairly high success.

The pin-penetration device is a minimally destructive instrument that is widely used to estimate the physical properties of wood, e.g., density, with advantages such as reduced testing times, low costs, and fewer defects induced in the wood being tested. In this study, such a device was used on 25 Indonesian hardwood species with a strength class (SC) distribution from SC II to IV (according to the Indonesian classification of wood SCs). Tests were conducted on three different orthogonal planes, i.e., cross-sectional, radial, and tangential planes. The wood density ranged from 0.28 to 0.88 g/cm3, and the specific gravity was 0.25 to 0.76. The cross-sectional plane penetration depth of the wood was significantly greater than that of either the radial or tangential plane, whereas the pin penetration values of the radial and tangential planes were not significantly different. A prediction model for predicting the density and specific gravity of wood via pin penetration showed a significant regression. Thus, the use of a pin-penetration device was found to be suitable for estimating wood density and specific gravity in a range of SCs of tropical wood species regardless of species.

Yulita KS, Susilowati A, Rachmat HH, Susila, Hidayat A, Dwiyanti FG. 2022. Molecular identification of Eurycoma longifolia Jack from Sumatra, Indonesia using trnL-F region. Biodiversitas 23: 1374-1382. Eurycoma longifolia Jack (Simaroubaceae) or pasak bumi is a popular medicinal plant from Southeast Asia’s rainforests that is used as an aphrodisiac, antimicrobial, anti-malaria antidiabetic, antiulcer, and anticancer agent. However, the increasing demand for this species for medicinal industries has led to illegal export in Indonesia. This study aimed to determine the specific genetic variation and develop DNA barcode using trnL-Fregion for E. longifolia originating from Sumatra, Indonesia. Twenty-two samples of the species were collected from four locations in Sumatra. An aligned sequence of the trnL-Fwas 960 bp with an A/T rich region (A: 30.2%, T: 34.5%, C: 16.7%, and G: 18.7%). The homology search using BLASTn of the GenBank NCBI showed that the nucleotide composition of the species was similar (99.9%) to the partial trnL-Fregion of E. longifolia MH751519 and E. apiculata GU593014. Close examination of the gene structure and composition showed that the DNA sequences have five nucleotides variations that were not possessed by the reference E. longifolia, and other taxa used. The obtained variations occurred mostly in the trnL intron region, and the phylogenetic analysis showed that the correct identity of the species of the samples by their position was at a similar clade as the other accessions of E. longifolia.

Sample collection activities for a study of population genetics across the natural distribution of targeted tree species require a lot of resources, mainly if repeated field visits are necessary. Conventionally, population genetic studies use good sample material like leaves. In addition, cambium or small pieces of fresh wood can be used to replace leaf samples. Currently, restrictions from the permit regulation have caused only a limited number of samples that can be collected. Therefore, efficient use of samples must be designed to maximize their uses for research. Due to the small amount of successfully sampled materials, hence there are limitations to extend their uses for other analyses and are often sufficient only for genetic analysis. Therefore, innovation in sampling methods using pickering punch (https://www.agroisolab.com/pickering-punch) to collect ebony wood cores in this study is required to cover multi-analyses not only limited to genetics but also for other analyses such as isotopes, near-infrared spectroscopy (NIRs), anatomy, and chemical compounds.•Pickering punch is recommended for efficient wood core sample collection from ebony standing trees.•323 wood core samples were successfully collected from 16 natural populations across Celebes (Sulawesi).•Multi-analyses studies on sampled wood cores are possible for ebony wood identification (e.g., species and origin/provenance).

Objectives Development of sequencing technology has opened up vast opportunities for tree genomic research in the tropics. One of the aforesaid technologies named ONT (Oxford Nanopore Technology) has attracted researchers in undertaking testings and experiments due to its affordability and accessibility. To the best of our knowledge, there has been no published reports on the use of ONT for genomic analysis of Indonesian tree species. This progress is promising for further improvement in order to acquire more genomic data for research purposes. Therefore, the present study was carried out to determine the effectiveness of ONT in generating long-read DNA sequences using DNA isolated from leaves and wood cores of Macassar ebony (Diospyros celebica Bakh.). Data description Long-read sequences data of leaves and wood cores of Macassar ebony were generated by using the MinION device and MinKnow v3.6.5 (ONT). The obtained data, as the first long-read sequence dataset for Macassar ebony, is of great importance to conserve the genetic diversity, understanding the molecular mechanism, and sustainable use of plant genetic resources for downstream applications.

Ebony (Diospyros celebica Bakh.) is an endemic plant on Celebes (Sulawesi) island. Extractive compounds within ebony wood cause it to have durability, strength, and beautiful patterns. In this study, we used near-infrared (NIR) spectroscopy to discriminate between ebony wood samples, based on their origins at different growth sites on Celebes island, and to develop quantitative models to predict the extractive content of ebony wood. A total of 45 wood meal samples from 11 sites located in West, Central, and South Celebes were collected in this study. NIR spectral data were acquired from hot water and ethanol&ndash, benzene soluble extracts from ebony wood in this study. The extractive content of the ebony was 10.408% and 10.774% based on hot water solubility and treatment with ethanol&ndash, benzene solvent, respectively. Multivariate analysis based on principal component analysis&ndash, discriminant analysis revealed that ebony wood from West Celebes differed from most of the wood from South Celebes, however, it was only slightly different from ebony wood from Central Celebes based on NIR spectra data. These findings were in line with the extractive contents obtained. Partial least square regression models based on wood meal spectra could potentially be used to estimate the hot water and ethanol&ndash, benzene extractive contents from ebony wood.

Objectives Efforts to restore tropical peat swamp forests in Indonesia face huge challenges of potential failures due to socio-economic factors and ecological dynamics attributed to lack of knowledge on the adaptive mechanisms of potential tree species such as Kapur (Dryobalanops aromatica C.F.Gaertn Syn. Dryobalanops sumatrensis J.F. Gmelin A.J.G.H Kostermans). This species is a multi-purpose tree that, commonly grows in mineral soils, but also in peat swamp as previously reported, which raised a fundamental question regarding the molecular mechanism of this adaptation. Therefore, a dataset was created aiming to detect candidates of adaptive genes in D. aromatica seedlings, cultivated in two contrasting potting media, namely mineral soil and peat media, based on RNA Sequencing Transcriptome Analysis. Data description The RNA transcriptome data of D. aromatica’s seedlings derived from young leaves of three one-year-old seedlings, raised in each dry mineral soil media and peat media, were generated by using Illumina HiSeq 4000 platform in NovogenAIT, Singapore. The acquired data, as the first transcriptome dataset for D. aromatica, is of a great importance in understanding molecular mechanism and responses of the involved genes of D. aromatica to the contrasting, growing potting media conditions that could also be useful to generate molecular markers.

Istomo, Kusmana C, Dwiyanti FG, Malik D. 2020. Comparison of several methods of stands inventory prior to logging towards the yield volume of mangrove forest in Bintuni Bay, West Papua Province, Indonesia. Biodiversitas 21: 1438-1447. The difference between the estimated volume and the actual harvested volume is the reason that mangrove forest management is unsustainable. To overcome this discrepancy, it is important to do what so called Inventarisasi Tegakan Sebelum Penebangan (ITSP) or stands inventory prior to logging for logging concession. However, the study on suitable ITSP methods for mangrove forests has been limited. This study aims to assess three ITSP methods (namely Line Strip Sampling Method, Line Systematic Sampling Method, and CIFOR’s Modified Method) using two allometric equations (i.e., equation developed specifically by a logging concession and equation developed that has specific formula for each species), and to select the combination of method and allometric equation that produce the highest accuracy for logging concession in mangrove forest, especially in Bintuni Bay, West Papua. The results showed that CIFOR’s Modified Method produces the lowest discrepancy between the estimated volume and the actual harvested volume, followed by Line Strip Sampling Method. In addition, regardless the ITSP methods employed, the allometric equation by Cole et al. (1999) outperforms the equation developed specifically by a logging concession. While producing the lowest discrepancy with plot size is the smallest than other methods, CIFOR’s Modified Method has a disadvantage when applied in the field due to difficulties in making a circular plot. As such, we recommend ITSP method to be used is the Line Strip Sampling method with allometric equation.

Large-scale genetic structure revealed in tree populations in SE Asia, as well as in many temperate forests, has been shaped by climatic fluctuation in the late Pleistocene, most importantly by that in the last glacial period. In a comparative study of the phylogeographic patterns of two closely related dipterocarp species, Dryobalanops aromatica C.F.Gaertn. and D. beccarii Dyer, we investigated how changes in land area associated with changes in climate affected large-scale genetic structure. We examined the genetic variation of D. aromatica, collected from nine populations throughout the Sundaic region, and of D. beccarii, collected from 16 populations mainly in Borneo, using seven polymorphic microsatellite markers. The two species were clearly distinguishable in the STRUCTURE analysis, although hybridisation probably occurred in sympatric populations and also in several other populations. The D. aromatica populations were divided into two main groups by the STRUCTURE analysis: Malay–Sumatra and Borneo. Mixing of the Sumatra and Borneo clusters occurred on the Malay Peninsula, supporting the hypothesis that tropical rainforests expanded over a dried Sunda Shelf during the last glacial period. The two main genetic clusters might have been formed by repeated cycles of fluctuation in land area. The D. beccarii populations in Borneo were divided into four geographically distinct groups: western Sarawak, central inland Sarawak, central coastal Sarawak and Sabah. The population on the Malay Peninsula (Gunung Panti) was an admixture of the four Bornean clusters. This suggests that this population is a relic of the recent range expansion of D. beccarii during the last glacial period.

Genetic variation and structure of Ubame oak (Quercus phillyraeoides A. Gray), a shrub tree on the Pacific coast of Japan, were examined to elucidate historical population dynamics using five chloroplast DNA (cpDNA) marker regions and 11 nuclear microsatellite loci. Three cpDNA haplotypes (A, B and C) were identified in a screen of 41 populations across the entire distribution range in Japan. Haplotype A was the most prevalent and was found in the entire range. Haplotype B was locally restricted to the Kii Peninsula, while haplotype C was restricted to the southwestern part of Japan. These haplotypes corresponded with the nuclear genetic constitution revealed by microsatellite markers. Two genetically differentiated major groups were identified by STRUCTURE analysis applied to 536 individuals from 28 populations, and they mostly corresponded with the two major cpDNA haplotypes, A and C. These populations were further divided into three geographically identified groups: group 1 in the area including Kanto and Tokai regions, the Kii Peninsula and the Muroto-misaki Cape on the Pacific coast; group 2 in the Bungo-suido Channel area; and group 3 in southern Kyushu and Okinawa. Populations in the Seto Inland Sea were divided into two groups: one was included in group 1 and appears to have originated from last glacial maximum (LGM) refugia located in the Kii Peninsula, while the other was included in group 2 and appears to have originated from LGM refugia located in southern Kyushu. These groups can be considered as conservation units for the preservation of unique seashore ecosystems, or as a seed source to foster coastal protection forests and next-generation production forests. Considerable care should be taken to protect isolated populations that may be specialized to unique local environments, such as those on the islands of Koshikijima and Izenajima.

Kapur (Dryobalanops aromatica) is an important dipterocarp species currently classified as vulnerable by the IUCN Red List Threatened Species. Science-based conservation and restoration efforts are needed, which can be supported by new genomic data generated from new technologies, including MinION Oxford Nanopore Technology (ONT). ONT allows affordable long-read DNA sequencing, but this technology is still rarely applied to native Indonesian forest trees. Therefore, this study aimed to generate whole genome datasets through ONT and use part of these data to construct the draft of the chloroplast genome and analyze the universal DNA barcode-based genetic relationships for D. aromatica. The method included DNA isolation, library preparation, sequencing, bioinformatics analysis, and phylogenetic tree construction. Results showed that the DNA sequencing of D. aromatica resulted in 1.55 Gb of long-read DNA sequences from which a partial chloroplast genome (148,856 bp) was successfully constructed. The genetic relationship was analyzed using two selected DNA barcodes (rbcL and matK), and its combination showed that species of the genus Dryobalanops had a close relationship as indicated by adjacent branches between species. The phylogenetic tree of matK and the combination of the matK and rbcL genes showed that D. aromatica was closely related to Dryobalanops rappa, whereas the rbcL gene showed group separation between D. aromatica and D. rappa. Therefore, a combination of the matK and rbcL genes is recommended for future use in the phylogenetic or phylogenomic analysis of D. aromatica.

Solar photovoltaics (PV) are on the rise even in areas of low solar insolation. However, in developing countries with limited capital, land scarcity, or with geographically isolated agrarian communities, large solar infrastructures are often impractical. In these cases, implementation of low-density PV over existing crops may be required to integrate renewable energy services into rural communities. Here, using Indonesia as a model system, we investigated the land use, energy, greenhouse gas emissions, economic feasibility, and the environmental co-benefits associated with off-grid solar PV when combined with high value crop cultivation. The life cycle analyses indicate that small-scale dual land-use systems are economically viable in certain configurations and have the potential to provide several co-benefits including rural electrification, retrofitting diesel electricity generation, and electricity for processing agricultural products locally. A hypothetical full-density off-grid solar PV for a model village in Indonesia shows that electricity output (1907.5 GJ yr−1) is much higher than the total residential consumption (678 GJ yr−1), highlighting the opportunity to downscale the PV infrastructure by half to lower capital cost, to co-locate crops, and to support secondary income generating activities. Economic analysis shows that the 30-year net present cost of electricity from the half-density co-located PV system (12,257 million IDR) is significantly lower than that of the flat cost of diesel required to generate equivalent electricity (14,702 million IDR). Our analysis provides insights for smarter energy planning by optimizing the efficiency of land use and limiting conversion of agricultural and forested areas for energy production.

Manurung J, Siregar IZ, Kusmana C, Dwiyanti FG. 2017. Genetic variation of the mangrove species Avicennia marina in heavy metal polluted estuaries of Cilegon Industrial Area, Indonesia. Biodiversitas 18: 1109-1115. Mangrove forests are often facing various anthropogenic disturbances, particularly in the industrial area. However, information on the status of industrial heavy metal pollution and its impact on the genetic variation of mangrove species, such as Avicennia marina, particularly in Indonesian industrial area has not been assessed. In this study, the classification of heavy metals in two estuaries of Cilegon Industrial Area (Pelabuhan Warna Sari and Krakatau) and one estuary outside Cilegon Industrial Area (Pulau Sangiang) were determined by Sediment Quality Guidelines- States Environment Protection Agency (SQGs-USEPA). Furthermore, the genetic diversity of 72 individuals of A. marina in the three estuaries were examined using four microsatellite loci (M3, M64, M81 and M98). The results showed that Krakatau area was the heavily polluted estuary based on SQGs-USEPA and have a lower genetic variation (He= 0.54) than Pelabuhan Warna Sari (moderately polluted, He= 0.56) and Pulau Sangiang (non-polluted, He= 0.60) suggesting a notable of deficiencies of genetic variation of A. marina in heavy polluted estuary compared to moderately and non-polluted estuary. Considering the low level of genetic variation in heavily polluted area, transplantation among estuaries and introduction of propagules from non-polluted estuary or other regions are needed as one of the conservation efforts.

The need for energy in Indonesia is increasingly growing into an inseparable part of the daily life of society. However, the limited availability of fossil fuel sources as raw materials for electricity and increased public awareness to preserve the environment lead to the need for an alternative source of renewable energy such as bioenergy, which is a renewable energy that utilizes biomass as its fuel source. Furthermore, this research was conducted to estimate the potential of biomass in Gunung Walat Education Forest (GWEF) as fuel for electricity generation. Estimation of the potential of electrical energy has been carried out by using the biomass conversion approach to wood pellets (WP). The results showed that Pinus merkusii stands have the highest biomass content (12,828.62 tons with a total area of 104 Ha) and Swietenia macrophylla stands have the lowest biomass content (16.63 tons with a total area of 0.67 Ha) compare to other stands. The total biomass obtained from 358.24 Ha of eleven stands was 45,041.38 tons and it can produce electricity of 123,863.79 MWh, suggesting that the biomass in GWEF has the potential to be developed to fulfill the electricity needs of 10.6 MWh per year.

Genetic variation and structure of Ubame oak (Quercus phillyraeoides A. Gray), a shrub tree on the Pacific coast of Japan, were examined to elucidate historical population dynamics using five chloroplast DNA (cpDNA) marker regions and 11 nuclear microsatellite loci. Three cpDNA haplotypes (A, B and C) were identified in a screen of 41 populations across the entire distribution range in Japan. Haplotype A was the most prevalent and was found in the entire range. Haplotype B was locally restricted to the Kii Peninsula, while haplotype C was restricted to the southwestern part of Japan. These haplotypes corresponded with the nuclear genetic constitution revealed by microsatellite markers. Two genetically differentiated major groups were identified by STRUCTURE analysis applied to 536 individuals from 28 populations, and they mostly corresponded with the two major cpDNA haplotypes, A and C. These populations were further divided into three geographically identified groups: group 1 in the area including Kanto and Tokai regions, the Kii Peninsula and the Muroto-misaki Cape on the Pacific coast; group 2 in the Bungo-suido Channel area; and group 3 in southern Kyushu and Okinawa. Populations in the Seto Inland Sea were divided into two groups: one was included in group 1 and appears to have originated from last glacial maximum (LGM) refugia located in the Kii Peninsula, while the other was included in group 2 and appears to have originated from LGM refugia located in southern Kyushu. These groups can be considered as conservation units for the preservation of unique seashore ecosystems, or as a seed source to foster coastal protection forests and next-generation production forests. Considerable care should be taken to protect isolated populations that may be specialized to unique local environments, such as those on the islands of Koshikijima and Izenajima.

The genus Dryobalanops Gaertn. f. is a small but important genus that contains seven species and is found in the Southeast Asian tropical rain forests. Seven polymorphic nuclear microsatellite markers were analyzed in 46 natural populations of six extant Dryobalanops species (N = 700 individuals) covering the distribution range in Western Malesia. The mean gene diversity at the species level ranged from 0.392 in D. rappa to 0.635 in D. aromatica. The FST value ranged from 0.156 in D. keithii to 0.283 in D. beccarii and all FST values were highly significantly greater than zero. These results suggest that gene flow between populations has been limited and intensive genetic drift has occurred in all of the species. Plants with narrowly distributed species such as D. keithii and D. rappa, which are endemic to Borneo, tend to have lower levels of genetic diversity compared with widespread species such as D. aromatica. STRUCTURE analysis revealed that at least two of the six species could be effectively discriminated each other. The results of this study will be helpful for building effective conservation schemes as well as for providing basic data for future provenance trials of Dryobalanops species.

DWIYANTI, F.G., KAMIYA, K. & HARADA, K. 2014. Phylogeographic structure of the commercially important tropical tree species Dryobalanops aromatica Gaertn. F. (Dipterocarpaceae) revealed by microsatellite markers. Reinwardtia 14(1): 43 – 51. ? Dryobalanops aromatica Gaertn. F. (Kapur) is an economically important timber species in Southeast Asia that can serve as a good model for studying the impact of the Pleistocene glaciations on the genetic diversity and distribution of species in tropical regions. Seven polymorphic microsatellite markers were analyzed in five natural populations of D. aromatica (N = 120 individuals): Gunung Panti in Malay Peninsula, Lingga Island in Lingga Archipelago, Lambir Hills National Park, Limbang and Similajau National Park in Borneo. The level of gene diversity (HE) for the five populations was relatively high with a range from 0.571 (Similajau) to 0.729 (Gunung Panti). The high genetic diversity in the present study could be attributed to the larger refugia population sizes of D. aromatica than that of other species. The population genetic structure revealed two distinct groups: the Malay Peninsula-Lingga Archipelago and Borneo. This pattern suggests that populations in each geographical area might be the consequence of post-glacial expansion from one or two refugia, but that gene flow between different glacial refugia was fairly restricted.

The existence of Dryobalanops sumatrensis and D. oblongifolia subsp. oblongifolia in Indonesia’s natural forest is increasingly threatened due to land use changes and illegal logging leading to the urgent need of conservation actions in the field. Vegetative propagation by shoot cuttings has been proposed as an alternative method, yet there have been still lacks of information regarding the suitable rooting media and the use of shoots from saplings as cutting materials. This study was to evaluate the survival rate, rooting and shoot sprouting abilites of D. sumatrensis and D. oblongifolia subsp. oblongifolia on two different media (mineral soil and peat). Saplings of the D. sumatrensis aged older than 7 years old and D. oblongifolia subsp. oblongifolia aged less than 2 years old were used as cutting materials. The results showed that the survival rate of D. sumatrensis in peat (43.75%) and mineral soil media (43.75%) was lower than D. oblongifolia subsp. oblongifolia in for peat media (54.55%) and minerals soil media (71.88%). The rooting and shoot sprouting percentage of D. sumatrensis in peat and mineral soil media was also lower than D. oblongifolia subsp oblongifolia. This pattern revealed that the media treatment (peat and minerals) did not affect the survival rate and rooting ability of D. sumatrensis shoot cuttings, but has an effect on D. oblongifolia subsp. oblongifolia.

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