Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：MDPI AG  

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.

DOI： 10.3390/f13040579

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

Shorea parvifolia (Dipterocarpaceae) is a widely distributed tree species which is important in terms of ecosystem functioning as well as forestry in Southeast Asia. During glacial periods, substantial precipitation decline is believed to have occurred in Southeast Asia, which considerably changed the distribution of the species. Repeated glacial and inter-glacial fluctuations were found to have influenced the genetic structure of the species, which is important to know for conservation and sustainable use. Leaf samples were collected from 18 populations covering most of the natural distribution of this species including the Malay Peninsula, Sumatra, and Borneo Islands. We investigated these samples using sequence data for eight chloroplast DNA (cpDNA) regions and 14 nuclear EST-SSR loci. The nucleotide diversity of cpDNA is higher in Malay Peninsula populations but the genetic diversity of nuclear DNA is higher in Borneo populations. The genetic structure revealed by nuclear DNA clearly separated Borneo populations from the rest, with an F-ST value of 0.150, while the genetic structure obtained from cpDNA was less pronounced (F-ST value = 0.136). Tajima's D and Fu and Li's D* for cpDNA showed statistical significance only in populations from Borneo. These results suggested that there has been recent population expansion of S. parvifolia in Borneo.

DOI： 10.1007/s11295-021-01525-8

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Other Link： https://link.springer.com/article/10.1007/s11295-021-01525-8/fulltext.html

Language：English   Publishing type：Research paper (scientific journal)  

© 2019, Society for Indonesian Biodiversity. All rights reserved. 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.

DOI： 10.13057/biodiv/d200635

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

A considerable extent of interspecific hybridization among dominant canopy dipterocarp species was recently found in a tropical rain forest fragment in Singapore. However, information about the fertility of the hybrids and the growth of their successive hybrids remains limited. We studied the flowering phenology of four dipterocarp species in the genus Shorea (S. curtisii, S. leprosula, S. parvifolia, and S. macroptera) and two hybrids (S. curtisii x S. leprosula and S. leprosula x S. parvifolia) and studied the performances of seedlings reproduced from them. We observed that S. macroptera bloomed first, without overlap with congeneric species, followed by the other Shorea species and the two first filial (F-1) hybrids. S. curtisii and S. leprosula, the species forming hybrids are most likely to succeed in this forest, completely overlapped with their hybrids. Fruits collected from the hybrids were viable, and these hybrid seedlings showed greater survival and a higher growth rate than those from pure species under greenhouse conditions. They included various cross types such as a backcross with each parent species. These results may imply that successive hybrids and introgression spontaneously occur among Shorea species. It may be important to consider the risk of hybridization for the management of tropical forests, particularly in degraded tropical rainforests where mechanisms of ecological isolation between closely related species might be altered.

DOI： 10.1016/j.foreco.2018.12.038

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© 2019 Forest Research Institute Malaysia. All rights reserved. Although cutting is a useful method for vegetative propagation and tree breeding, there is a difference in rooting ability between tree species and even between node positions within a species. A large number of F1 hybrids of Shorea (Shorea curtisii × S. leprosula) (Dipterocarpaceae) have recently been found in Singapore. Given that some of the hybrid traits appear to have higher physiological performances than those of their parent species, understanding the rooting ability of the leafy-stem cuttings of F1 hybrids may contribute to performance improvement in dipterocarp trees. In this study, we compared the rooting abilities of cuttings taken from seedlings of F1 hybrids and their parent species at different node positions. The cuttings of F1 hybrids showed rooting ability with small internode differences, and the rooting rate (32.2%) was almost intermediate between those of S. curtisii (42.0%) and S. leprosula (21.0%). The rooting rates of hybrids and parents fell into the middle range of previously reported values for 21 closely related Shorea species. Overall, the rooting ability of F1 hybrids is comparable with that of their parent species and/or other Shorea species in the red meranti group. Thus, F1 hybrids could be mass propagated through cuttings.

DOI： 10.26525/jtfs2019.31.3.324

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DOI： 10.1266/ggs.17-00026

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Royal Botanic Garden Edinburgh  

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.

DOI： 10.24823/sibbaldia.2018.255

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：GENETICS SOC JAPAN  

Geographical variation in soil bacterial community structure in 26 tropical forests in Southeast Asia (Malaysia, Indonesia and Singapore) and two temperate forests in Japan was investigated to elucidate the environmental factors and mechanisms that influence biogeography of soil bacterial diversity and composition. Despite substantial environmental differences, bacterial phyla were represented in similar proportions, with Acidobacteria and Proteobacteria the dominant phyla in all forests except one mangrove forest in Sarawak, although highly significant heterogeneity in frequency of individual phyla was detected among forests. In contrast, species diversity (alpha-diversity) differed to a much greater extent, being nearly six-fold higher in the mangrove forest (Chao' index = 6,862) than in forests in Singapore and Sarawak (similar to 1,250). In addition, natural mixed dipterocarp forests had lower species diversity than acacia and oil palm plantations, indicating that aboveground tree composition does not influence soil bacterial diversity. Shannon and Chaol indices were correlated positively, implying that skewed operational taxonomic unit (OTU) distribution was associated with the abundance of overall and rare (singleton) OTUs. No OTUs were represented in all 28 forests, and forest -specific OTUs accounted for over 70% of all detected OTUs. Forests that were geographically adjacent and/or of the same forest type had similar bacterial species composition, and a positive correlation was detected between species divergence (beta-diversity) and direct distance between forests. Both alpha- and beta-diversities were correlated with soil pH. These results suggest that soil bacterial communities in different forests evolve largely independently of each other and that soil bacterial communities adapt to their local environment, modulated by bacterial dispersal (distance effect) and forest type. Therefore, we conclude that the biogeography of soil bacteria communities described here is non-random, reflecting the influences of contemporary environmental factors and evolutionary history.

DOI： 10.1266/ggs.16-00013

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Society for Indonesian Biodiversity  

Genetic variation is considered to be the key factor for longterm survival of the species. The recognition of the existing genetic diversity is the preliminary phase in development of an effective strategy for conservation of forest tree species. Taxus sumatrana or is confined to grow naturally only in Asia, it is a rare and endangered species that in several Asian countries needs both ex situ and in situ protection program. In its natural distribution, T. sumatrana is the only Taxus species that reached its southernmost distribution to Sumatran forest-Indonesia and locally named as Sumatran Yew. The objective of this research was to determine the genetic variation of T. sumatrana as baseline information for designing conservation strategy of the species. Leaves samples were collected from two natural population of T. sumatrana in Mt. Kerinci (Sungai Penuh, Jambi) and Mt. Dempo (Pagaralam, South Sumatra), both sites are located along Bukit Barisan Mountain Ranges of Sumatra. We sequenced two non-coding chloroplast DNA (cpDNA) regions of trnL-trnF and psbC-trnS that each yielded 808 bp and 1092 bp, and rbcL gene of 523 bp, in which the total length covered 2423 bp. Surprisingly, we found no variation for all individuals and population, which means that the species is similar and both populations are not genetically structured. This study also revealed on how a proper conservation strategy should be practiced for the species as we know that without a sufficient amount of genetic variation, a population cannot evolve in response to changing environmental conditions. In situ conservation program is a must that can maintain the existence of the species while at the same time keeping the sustainability of the entire systems
in other side ex situ conservation strategy can take place as an additional effort to secure the genetic resources in case of the catastrophic events that might diminish their limited natural habitat.

DOI： 10.13057/biodiv/d170213

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER JAPAN KK  

The vertical structure of a tropical rain forest is complex and multilayered, with strong variation of micro-environment with height up to the canopy. We investigated the relation between morphological traits of leaf surfaces and tree ecological characteristics in a Malaysian tropical rain forest. The shapes and densities of stomata and trichomes on the abaxial leaf surfaces and their relation with leaf characteristics such as leaf area and leaf mass per area (LMA) were studied in 136 tree species in 35 families with different growth forms in the tropical moist forest. Leaf physiological properties were also measured in 50 canopy and emergent species. Most tree species had flat type (40.4 %) or mound type (39.7 %) stomata. In addition, 84 species (61.76 %) in 22 families had trichomes, including those with glandular (17.65 %) and non-glandular trichomes (44.11 %). Most leaf characteristics significantly varied among the growth form types: species in canopy and emergent layers and canopy gap conditions had higher stomatal density, stomatal pore index (SPI), trichome density and LMA than species in understory and subcanopy layers, though the relation of phylogenetically independent contrasts to each characteristic was not statistically significant, except for leaf stomatal density, SPI and LMA. Intrinsic water use efficiency in canopy and emergent tree species with higher trichome densities was greater than in species with lower trichome densities. These results suggest that tree species in tropical rain forests adapt to a spatial difference in their growth forms, which are considerably affected by phylogenetic context, by having different stomatal and trichome shapes and/or densities.

DOI： 10.1007/s10265-016-0795-2

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：TAYLOR & FRANCIS LTD  

Background: Although natural hybridisation between dipterocarp trees is considered rare, putative dipterocarp hybrids (Shorea spp.) are found in a forest fragment in Singapore. Understanding the performance of hybrids is critical to inform conservation efforts and has implications for the demographic and genetic viability of these small populations. Aims: First, is there a difference in the frequency of hybrids between the mature and seedling stages, and second, do parent and hybrid seedlings have different ecological traits?
Methods: We analysed seedling survival and growth rates in relation to environmental variables for Shorea curtisii, S. leprosula and hybrids of the two species. We monitored the height and diameter of seedlings for 4 years, as well as light conditions and soil moisture.
Results: The proportion of hybrids at the seedling stage was 41% for S. leprosula and 17% for S. curtisii, respectively. Hybrids were more frequent at the seedling stage than at the mature stage. Hybrid individuals had growth and survival rates comparable to their parent species, with the exception of slower growth rates than S. leprosula.
Conclusions: Hybrid seedlings lacked obvious heterosis, and might therefore have similar fitness to that of parent species in the present forest environment.

DOI： 10.1080/17550874.2016.1265606

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SustaiN Society  

DOI： 10.24910/jsustain/3.1/1220

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Indonesian Institute of Sciences  

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.

DOI： 10.14203/reinwardtia.v14i1.394

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Seameo Biotrop  

Dipterocarpus littoralis Blume is a critically endangered dipterocarp species found only in Nusakambangan Island, Central Java, Indonesia. Patterns of genetic diversity and population genetic structure of adults and saplings in two extant populations (Kali Jati and Solok Besek) were estimated using ten microsatellite markers. A total of 39 alleles were found, with two and four alleles being unique in adult and sapling populations, respectively. Allelic richness and heterozygosity were similar between adult (Ar = 3.00
= He 0.423) and sapling (Ar= 3.25
He = 0.441) populations. Inbreeding coefficients in saplings were positive in both populations and statistically significant in Kali Jati, while those in adult populations were not significantly different from zero, indicating excessive inbreeding and selfing in the sapling populations. Genetic differentiation of the sapling populations (FST= 0.036) was slightly lower than in the adult populations (0.050), but only significantly so for saplings. This study revealed that D. littoralis has low genetic diversity in both adults and saplings. Similarly low values in allele richness and heterozygosity suggest that reductions of population size have been ongoing for long periods in this species. Significant genetic differentiation between sapling populations but not adult populations indicates that recent fragmentation is further accelerating the isolation process.

DOI： 10.11598/btb.2014.21.1.1

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PUBLIC LIBRARY SCIENCE  

There are very few studies that have investigated host-specificity among tropical herbivorous insects. Indeed, most of the trophic interactions of herbivorous insects in Southeast Asian tropical rainforests remain unknown, and whether polyphagous feeding is common in the herbivores of this ecosystem has not been determined. The present study employed DNA bar coding to reveal the trophic associations of adult leaf-chewing chrysomelid beetles in a Bornean rainforest. Plant material ingested by the adults was retrieved from the bodies of the insects, and a portion of the chloroplast rbcL sequence was then amplified from this material. The plants were identified at the family level using an existing reference database of chloroplast DNA. Our DNA-based diet analysis of eleven chrysomelid species successfully identified their host plant families and indicated that five beetle species fed on more than two families within the angiosperms, and four species fed on several families of gymnosperms and/or ferns together with multiple angiosperm families. These findings suggest that generalist chrysomelid beetles associated with ecologically and taxonomically distant plants constitute a part of the plant-insect network of the Bornean rainforest.

DOI： 10.1371/journal.pone.0074426

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER JAPAN KK  

In order to elucidate the phylogeographical relationships and to find the past colonization routes of evergreen oak (Quercus phillyraeoides), we collected samples from 19 populations from the central to western part of Japan and examined chloroplast DNA sequence variation. We analyzed the genetic variation for four non-coding and one coding region and examined a total of 3,665 bp. Total nucleotide diversity (pi) was 0.00017 +/- A 0.00001, and the scaled mutation rate (theta (w)) was 0.00021 +/- A 0.00011. These values were relatively smaller than those formerly reported for Japanese deciduous oak species (Q. mongolica var. crispula). A total of five haplotypes, two of which included two subtypes (A1, A2, B, C, D1, D2, E), were identified, with types A1 and D2 the most frequent. A large degree of genetic differentiation had occurred across the populations (G (ST) = 0.833 for haplotype data and F (ST) = 0.858 for sequence data). The data suggested several possible refugia populations on the Pacific Ocean coast and the East China Sea coast, nearly identical to those previously suggested for the lucidophyllus forest refugia. We could not find any evidence showing that any part of the Seto Inland Sea populations could be possible refugia. Largest genetic differentiation across the populations in the Seto Inland Sea region suggests that these areas have been recently colonized following the last glacial maximum from the refugia in the Pacific coast or in southern Kyushu.

DOI： 10.1007/s10310-012-0357-y

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

Tropical rainforests in South-East Asia have been affected by climatic fluctuations during past glacial eras. To examine how the accompanying changes in land areas and temperature have affected the genetic properties of rainforest trees in the region, we investigated the phylogeographic patterns of a widespread dipterocarp species, Shorea leprosula. Two types of DNA markers were used: expressed sequence tag-based simple sequence repeats and chloroplast DNA (cpDNA) sequence variations. Both sets of markers revealed clear genetic differentiation between populations in Borneo and those in the Malay Peninsula and Sumatra (Malay/Sumatra). However, in the south-western part of Borneo, genetic admixture of the lineages was observed in the two marker types. Coalescent simulation based on cpDNA sequence variation suggested that the two lineages arose 0.280.09million years before present and that following their divergence migration from Malay/Sumatra to Borneo strongly exceeded migration in the opposite direction. We conclude that the genetic structure of S.leprosula was largely formed during the middle Pleistocene and was subsequently modified by eastward migration across the subaerially exposed Sunda Shelf.

DOI： 10.1111/mec.12243

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

We assessed the variability of chloroplast DNA sequences in populations of the dipterocarp forest tree, Shorea curtisii. This species is widely distributed in hill and coastal hill dipterocarp forests of the Malay Peninsula, whereas isolated populations are found in the coastal hills of north Borneo. Two chloroplast DNA regions (1555 similar to bp of trnH-psbA-trnK and 925 similar to bp of trnL-trnF) were sequenced from 123 individuals collected from six Malay Peninsula and two Bornean populations. There were 15 chloroplast haplotypes derived from 16 polymorphic sites. A haplotype network revealed two distinct haplogroups that correlate with two geographic regions, the Malay Peninsula and Borneo. These two haplogroups differed by a number of mutations, and no haplotypes were shared between populations from the different geographic regions. This suggests an ancient diversification of these haplogroups, and that long-distance seed dispersal was unlikely to have occurred during the Pleistocene when the Sunda Shelf was a contiguous landmass. Phylogenetic analysis of the haplotypes together with those found in other Shorea species showed that two haplogroups in S. curtisii appear in different positions of the phylogenetic tree. This could be explained by the persistence of ancestral polymorphisms or by ancient chloroplast capture. Low levels of genetic differentiation were found between populations within each geographic region. Signature of a bottleneck followed by demographic expansion was detected in the Malay Peninsula haplogroup. The presence of two distinct evolutionary lineages in the different regions suggests that they should be managed independently to conserve the major sources of genetic diversity in S. curtisii.

DOI： 10.1111/j.1744-7429.2011.00834.x

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Shoreajavanica (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 veiy 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-trnfhl and two non-coding chloroplast DNA regions of trnY-trriL, 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 (FST = 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. © 2012 Asian Network for Scientific Information.

DOI： 10.3923/pjbs.2012.783.788

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER HEIDELBERG  

Shorea (Dipterocarpaceae) is a large genus in which many closely related species often grow together in Southeast Asian lowland tropical rain forests. Many Shorea species share common pollinators, and earlier studies suggested occurrence of interspecific hybridization and introgression. Here, we show morphological and molecular evidence of hybridization between Shorea species. In the census of all the trees of Shorea curtisii, Shorea leprosula, and Shorea parvifolia (> 30 cm dbh) within the 164-ha area of Bukit Timah Nature Reserve in Singapore, we found 21 morphologically recognizable hybrid individuals. All of the putative hybrids could be distinguished obviously from the parental species on the basis of vegetative characters. Population genetic analysis of DNA sequences of two nuclear (GapC and PgiC) and chloroplast (trnL-trnF) regions demonstrated that each of the three species had several species-specific mutations. The nuclear sequences of the putative hybrids were heterozygote at all the species-specific sites between two parental species. Hybrid between S. curtisii and S. leprosula was found most, while S. curtisii x S. parvifolia and S. leprosula x S. parvifolia hybrids were also found. Almost no shared polymorphism between populations of the parental species suggests rarity of introgression. The study indicated that natural hybridization between sympatric Shorea species should not be uncommon, but all of the hybrid individuals were F(1), and the post-F(1) hybrids were considerably rare.

DOI： 10.1007/s11295-010-0332-8

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER TOKYO  

The extent of tropical forest has been declining, due to over-exploitation and illegal logging activities. Large quantities of unlawfully extracted timber and other wood products have been exported, mainly to developed countries. As part of the export monitoring effort, we have developed methods for extracting and analyzing DNA from wood products, such as veneers and sawn timbers made from dipterocarps, in order to identify the species from which they originated. We have also developed a chloroplast DNA database for classifying Shorea species, which are both ecologically and commercially important canopy tree species in the forests of Southeast Asia. We are able to determine the candidate species of wood samples, based on DNA sequences and anatomical data. The methods for analyzing DNA from dipterocarp wood products may have strong deterrent effects on international trade of illegitimate dipterocarp products. However, the method for analyzing DNA from wood is not perfect for all wood products and need for more improvement, especially for plywood sample. Consequently, there may be benefits for the conservation of tropical forests in Southeast Asia.

DOI： 10.1007/s10265-010-0348-z

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The Drosophila ananassae species cluster includes D. ananassae, D. pallidosa, D. parapallidosa, and the cryptic species "pallidosa-like", "pallidosa-like Wau", and "papuensis-like". Some of the taxa are sympatric in the South Pacific, Papua New Guinea, and Southeast Asia, and gene flow between different taxa has been suspected for a handful of genes. In the present analysis, we examined DNA sequences of introns in four loci: alpha actinin (Actn) on XL, white (w) on XR, CG7785 on 2L, and zinc ion transmembrane transporter 63C (ZnT63C) on 2R. Phylogenetic trees (neighbor-joining and haplotype network) were inconsistent among these loci. Some haplotypes shared between taxa were found for w, CG7785, and ZnT63C, suggesting recent gene flow. However, no haplotypes were shared, for example, between D. ananassae and D. pallidosa for CG7785, which is close to the proximal breakpoint of In(2L) D. This suggests that taxon-specific inversions prevent gene flow, as predicted by the chromosomal speciation hypothesis.

DOI： 10.2108/zsj.27.303

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

Cichlid fishes in Lake Victoria show spectacular diversification that is thought to be recent. Therefore, by investigating those fishes, we may be able to elucidate recently completed or ongoing speciation processes. We studied the population structures of two closely related pelagic cichlid species, Haplochromis pyrrhocephalus and H. laparogramma, using a mitochondrial DNA locus and 12 nuclear microsatellite loci as putative neutral markers. Ten and two populations of H. pyrrhocephalus and H. laparogramma, respectively, were sampled from the southern part of Lake Victoria. We grouped those 12 populations into four mutually differentiated regional populations, one of which consisted of the two H. laparogramma populations. The levels of differentiation were substantial at the mitochondrial locus (F(ST)=0.03-0.54), but very low at microsatellite loci (R(ST)=0.008-0.116). The data from both types of loci indicated that the regional population of H. laparogramma was first separated from those of H. pyrrhocephalus if we set aside one erratic population of H. pyrrhocephalus. The data also suggested recent population expansions of the two species, the time scales for which were estimated to be on the order of 10(4)-10(5) years. These data suggested that dynamic speciation processes accompanied occasional spawning of new species and population size changes in this lake. (C) 2008 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.gene.2008.11.008

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL PUBLISHING, INC  

Nine microsatellite markers were developed for Zanthoxylum ailanthoides, a typical pioneer tree. Averaged over the nine loci, the number of alleles per locus was 5.1. The observed and expected heterozygosities ranged from 0.233 to 0.833 and from 0.314 to 0.823, with averages of 0.606 and 0.641, respectively. No loci showed significant departures from Hardy-Weinberg equilibrium or linkage equilibrium after Bonferroni correction (P > 0.05). These markers will be useful for parentage analyses and studies of population genetic structure in the species.

DOI： 10.1111/j.1755-0998.2008.02507.x

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ACADEMIC PRESS INC ELSEVIER SCIENCE  

A pseudogene with 94% similarity to mitochondrial cytochrome c oxidase subunit I (COI) was identified and localized to chromosome 4 of Drosophila ananassae. Because this chromosome is believed to have reduced recombination, its history can be traced using the pseudo-COI sequence. Pseudo-COI sequences were obtained from 27 iso-female lines of six taxa belonging to the D. ananassae species cluster in which reproductive isolation is incomplete. The phylogenetic network constructed from seven recognized haplotypes (#0-#6) indicated that different taxa inhabiting the same geographic area share the haplotypes: #1 from Papua New Guinean populations of D. ananassae and pallidosa-like-Wau; #2 from Papua New Guinean populations of D. ananassae, pallidosa-like, and papuensis-like; and #4 from South Pacific populations of D. ananassae and D. pallidosa. Taxon-K has a unique haplotype (#6), and 18 mutation steps separate it from the closest haplotype, #2. We discuss the possibility of chromosome 4 introgression beyond taxon boundaries. (C) 2008 Elsevier Inc. All rights reserved.

DOI： 10.1016/j.ympev.2008.06.007

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY  

Differences in demographic history, life-history traits, and breeding systems affect nucleotide variation patterns. It is expected that shade-intolerant pioneer tree species have different patterns of genetic polymorphism and population structure than climax species. We studied patterns of nucleotide polymorphism at four putative starch pathway loci (agpSA, agpSB, agpL, and GBSSI) in Zanthoxylum ailanthoides, a shade-intolerant pioneer tree species that occupies forest gaps in warm-temperate forests of East Asia. Genetic diversity was lower within each population than among populations, and differentiation among populations was high across the loci (F-ST = 0.32-0.64), as expected from the insect-pollinated breeding system and the metapopulation structure of this pioneer species. Numbers of haplotypes were smaller than those expected from the observed numbers of segregating sites. Single haplotypes accounted for more than 47% of all the sampled genes at the respective loci. These variation patterns were incompatible with neutral predictions for populations of a finite island model. Complex population dynamics, such as bottleneck and/or admixture, in the history of this pioneer tree species might have resulted in the observed patterns of genetic variation and population structure, which are different from those of climax wind-pollinated tree species, such as conifers. In contrast to the other loci investigated in this study, agpL showed nearly no variation in Z. ailanthoides (one singleton only), but there was some extent of variation in a closely related species, Zanthoxylum schinifolium. This suggests possibly a recent selective sweep at or near the locus in Z. ailanthoides.

DOI： 10.1111/j.1365-294X.2008.03756.x

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Language：English   Publisher：GENETICS SOC JAPAN  

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：BOTANICAL SOC AMER INC  

Dipterocarpaceae. trees that dominate tropical rain forests in Southeast Asia consist of many economically and ecologically important species. We determined partial sequences of the PgiC gene from species of Shorea, Hopea, Neobalanocarpus. and Parashorea to elucidate phylogenetic relationships among the species of these genera, which have been regarded as interrelated. The sequences generated a gene tree with better resolution than previous cpDNA trees. The PgiC tree is essentially consistent with cpDNA trees, except for the placement of Neobalanocarpus. The PgiC tree shows that Neobalanocarpus is nested within White Meranti of Shorea, whereas this genus forms a clade with Hopea in cpDNA trees. This conflict suggests that Neobalanocarpus is derived via hybridization between White Meranti of Shorea and Hopea. Species belonging to each of three timber groups (Yellow Meranti, Balau, and Red Meranti) within Shorea are monophyletic. Together they form a monophyletic clade distinct from White Meranti. Botanical sections within Red Meranti appear not to be monophyletic. An extensive number of shared polymorphisms among species and consequential lack of monophyly of intraspecific haplotypes are found in Red Meranti. Potential causes of this phenomenon, including persistence of ancestral polymorphisms and gene flow via interspecific hybridization. are discussed.

DOI： 10.3732/ajb.92.5.775

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The plastid DNA sequences of rbcL, matK, the trnV intron and the rpl20-rps18 spacer were analyzed among 39 species of subgenus Pinus. A total of 3932 bp were used to assess relationships using MP, NJ and ML algorithms. Subgenus Pinus splits into two distinct lineages, corresponding to Eurasia and North America ("New World hard pines"). The Eurasian lineage was differentiated into two clades; the Mediterranean pines including the Himalayan pine, P. roxburghii (subsections Canarienses, Pinea, Halepenses, and Pinaster), and subsection Pinus. Two North American pines, P. tropicalis and P. resinosa, are typical members of subsection Pinus but did not cluster together. Subsection Contortae occupied the basal position in the "New World hard pines" followed by subsection Ponderosae. The members of subsection Australes from south of U.S. formed a strongly supported clade sister to the remaining species. Of remaining "New World hard pines" subsections, Attenuatae was a monophyletic group, and Oocarpae, Leiophyllae and Australes (Florida/Caribbean species) were poorly resolved. Autrales was paraphyletic in our phylogeny. The divergence times for each subsection were estimated from the rbcL sequence data. © Arbora Publishers.

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：CAMBRIDGE UNIV PRESS  

DOI： 10.1017/S0266467404001713

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：UNIV CHICAGO PRESS  

The plastid DNA sequences of rbcL, matK, the trnV intron, and the rpl20-rps18 spacer in 38 species of subgenus Pinus, representing all recognized subsections, were analyzed. Combined data sets of 3230 bp were used to assess relationships with maximum parsimony, neighbor joining, and maximum likelihood algorithms. Subgenus Pinus splits into two distinct lineages, corresponding to Eurasia and North America ("New World hard pines"). The Eurasian lineage differentiated into two clades: the Mediterranean pines, including the Himalayan pine P. roxburghii (subsections Canarienses, Halepenses, and Pinaster), and subsection Pinus. Two North American pines, P. tropicalis and P. resinosa, are typical members of subsection Pinus but are not closely related to each other. Subsection Contortae occupied the basal position in the "New World hard pines" followed by subsection Ponderosae. Of the remaining "New World hard pines" subsections, Attenuatae was a monophyletic group and Oocarpae, Australes, and Leiophyllae were poorly resolved. The eastern Cuban pines, P. cubensis and P. maestrensis, formed a subgroup within Australes. matK evolved much faster than rbcL, and the noncoding regions evolved more slowly than rbcL and matK synonymous sites. The divergence times for each subsection were estimated from the rbcL sequence data calibrated by fossil data.

DOI： 10.1086/342213

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：GENETICS SOC JAPAN  

The genetic variation of Trigonobalanus verticillata, the most recently described genus of Fagaceae, was studied using chloroplast DNA sequences and AFLP fingerprinting. This species has a restricted distribution that is known to include seven localities in tropical lower montane forests in Malaysia and Indonesia. A total of 75 individuals were collected from Bario, Kinabalu, and Fraser's Hill in Malaysia. The sequences of rbcL, matK, and three non-coding regions (atpB-rbcL spacer, trnL intron, and trnL-trnF spacer) were determined for 19 individuals from these populations. We found a total of 30 nucleotide substitutions and four length variations, which allowed identification of three haplotypes characterizing each population. No substitutions were detected within populations, while the tandem repeats in the trnL-trnF spacer had a variable repeat number of a 20-bp motif only in Kinabalu. The differentiation of the populations inferred from the cpDNA molecular clock calibrated with paleontological data was estimated to be 8.3 MYA between Bario and Kinabalu, and 16.7 MYA between Fraser's Hill and the other populations. In AFLP analysis, four selective primer pairs yielded a total of 431 loci, of which 340 (78.9%) were polymorphic. The results showed relatively high gene diversity (H-S=0.153 and H-T=0.198) and nucleotide diversity (pi(S)=0.0132 and pi(T)=0.0168) both within and among the populations. Although the cpDNA data suggest that little or no gene flow occurred between the populations via seeds, the fixation index estimated from AFLP data (F-ST=0.153 and N-ST=0.214) implies that some gene flow occurs between populations, possibly through pollen transfer.

DOI： 10.1266/ggs.77.177

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ACADEMIC PRESS INC  

To obtain a refined molecular phylogeny of dipterocarp species in Southeast Asia, nucleotide sequences of matK, the intron of trnL, and intergenic spacer region between trnL and trnF in chloroplast DNA were determined in 16 species throughout 10 genera. In the resultant trees Southeast Asian dipterocarp species were divided into two clusters. One cluster consisted of Anisoptera, Vatica, Cotylelobium, and Upuna, all with the base chromosome number of x = 11. The second cluster consisted of Hopea, Shorea, Neobalanocarpus, Dryobalanops, Parashorea, and Dipterocarpus, mostly with the base chromosome number of x = 7. Dipterocarpus was the only genus that had the base chromosome number x = 11 in the latter cluster. This result suggests that the chromosome number changed from x = 11 to x = 7 after Dipterocarpus branched in the latter cluster. Other evolutionary changes of morphological characters are also discussed. (C) 1998 Academic Press.

DOI： 10.1006/mpev.1998.0516

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Language：English  

DOI： 10.3759/tropics.7.195

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Publishing type：Research paper, summary (national, other academic conference)   Publisher：THE JAPANESE FORESTRY SOCIETY  

<p>[in Japanese]</p>

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Language：English   Publishing type：Research paper, summary (national, other academic conference)   Publisher：GENETICS SOC JAPAN  

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Language：English   Publisher：Forest Department Sarawak (FDS); Japan Research Consortium for Tropical Forests in Sarawak (JRCTS)  

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：GENETICS SOC JAPAN  

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Language：Japanese   Publisher：THE JAPANESE FORESTRY SOCIETY  

劣化熱帯林の修復には郷土樹種のエンリッチメント植栽が効果的である。本研究では郷土樹種の生態特性解明のため、光環境と苗の成長や生理特性を比較した。調査はマレー半島の劣化林で行ない、様々な光環境に、キョウチクトウ科の<i>Dyera costulata</i> (DC)、フタバガキ科の<i>Dipterocarpus baudii</i> (DB), <i>Neobalanocarpus heimii</i> (NH)とジンチョウゲ科の<i>Gonystylus affinis </i>(GA)を植栽した。植栽後7年間、樹高と直径を測定し、光合成や最大光量子収率も測定した。DCとDBでは開空度が35％以上の明環境で成長がよく、NBでは15-35％程度で高くなった。光合成速度(<i>P</i><sub>max</sub>)が最大になる開空度はDC、DBが30％以上、NB、GAは20％程度であった。後者は開空度35％以上で強光阻害を受けた。以上からDCとDBは開空度30-40％の明環境が、NHとGAは開空度20％程度の被陰環境が好ましいと考えられた(Kenzo et al. 2011 Journal of Tropical Forest Science 23:271-281)。

DOI： 10.11519/jfsc.124.0.715.0

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：GENETICS SOC JAPAN  

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Language：Japanese   Publishing type：Article, review, commentary, editorial, etc. (scientific journal)   Publisher：日本森林学会  

DOI： 10.11519/jjsk.62.0_3

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Language：Japanese   Publisher：THE JAPANESE FORESTRY SOCIETY  

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Language：Japanese   Publishing type：Article, review, commentary, editorial, etc. (scientific journal)  

DOI： 10.11519/jjsk.60.0_39

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Language：English  

DOI： 10.3759/tropics.13.119

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